Grazie a voi Kevin Miyashiro per la placcatura e il mantenimento di colture cellulari, al Dott. Terri Schochet per la fornitura di colture cellulari per le immagini incluse in questo documento. Inoltre, grazie a Kevin Miyashiro, Dr. Peter Buckley, e Tiina Pertiz per l&#39;ingresso sulla procedura ARNA. Il finanziamento per questo lavoro è stato dal National Institute on Aging, l&#39;Istituto Nazionale per la Salute Mentale e Risorse Umane fondi Fact Finder dal Commonwealth della Pennsylvania.

<ol>
	<li>Davis, J. E., Eberwine, J. H., Hinkle, D. A., Marciano, P. G., Meaney, D. F., McIntonsh, T. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methodological+considerations+regarding+single-cell+gene+expression+profiling+for+brain+injury.">Methodological considerations regarding single-cell gene expression profiling for brain injury.</a> Neurochemical Research. 29, 1113-1121 (2004).</li><li>Eberwine, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+molecular+biology.">Single-cell molecular biology.</a> Nature Neuroscience. 4, 1155-1156 (2001).</li><li>Kamme, F., Salunga, R., Yu, J., Tran, D., Zhu, J., Luo, J., Bittner, A., Guo, H., Miller, N., Wan, J., Erlander, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+microarray+analysis+in+hippocampus+CA1:+Demonstration+and+Validation+of+Cellular+Heterogeneity.">Single-cell microarray analysis in hippocampus CA1: Demonstration and Validation of Cellular Heterogeneity.</a> The Journal of Neuroscience. 23, 3607-3607 (2003).</li><li>Hinkle, D., Glanzer, J., Sarabi, A., Pajunen, T., Zielinski, J., Belt, B., Miyashiro, K., McIntosh, T., Eberwine, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+neurons+as+experimental+systems+in+molecular+biology.">Single neurons as experimental systems in molecular biology.</a> Progress in Neurobiology. 72, 129-142 (2004).</li><li>Ginsberg, S. D., Elarova, I., Ruben, M., Tan, F., Counts, S. E., Eberwine, J. H., Trojanowski, J. Q., Hemby, S. E., Mufson, E. J., Che, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+gene+expression+analysis:+Implications+for+Neurodegenerative+and+Neuropsychiatric+Disorders.">Single-cell gene expression analysis: Implications for Neurodegenerative and Neuropsychiatric Disorders.</a> Neeurochemical Research. 29, 1053-1064 (2004).</li><li>Eberwine, J., Spencer, K., Miyashirto, K., Mackler, S., Finnell, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Complementary+DNA+synthesis+in+situ:+methods+and+applications.">Complementary DNA synthesis in situ: methods and applications.</a> Methods Enxymol. 216, 80-100 (1992).</li><li>Eberwine, J., Yeh, H., Miyashiro, K., Cao, Y., Nair, S., Finnell, R., Zettel, M., Coleman, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+gene+expression+in+single+live+neurons.">Analysis of gene expression in single live neurons.</a> Proc. Natl. Acad. Sci. USA. 89, 3010-3014 (1992).</li><li>Kelz, M. B., Dent, G. W., Therianos, S., Marciano, P. G., McIntosh, T. K., Coleman, P. D., Eberwine, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+antisense+RNA+amplification+and+microarray+analysis+as+a+tool+for+studying+neurological+degeneration+and+restoration.">Single-cell antisense RNA amplification and microarray analysis as a tool for studying neurological degeneration and restoration.</a> Sci. Aging Knowledge Eviron. 1, re1-re1 (2002).</li><li>Banker, G. A., Cowan, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rat+hippocampal+neurons+in+dispersed+cell+culture.">Rat hippocampal neurons in dispersed cell culture.</a> Brain Research. 126, 397-425 (1977).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> P-1000 &#38; P-97 Pipette Cookbook. , (2010).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> MinElute Handbook For MinElute Reaction Cleanup Kit. , 28-29 (2004).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Megascript kit. , 7-8 .</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> MEGAclear kit. , 4-5 .</li><li>Eberwine, J., Kacharmina, J. E., Andrews, C., Miyashiro, K., McIntosh, T., Becker, K., Barrett, T., Hinkle, D., Dent, G., Marciano, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=mRNA+expression+analysis+of+tissue+sections+and+single+cells.">mRNA expression analysis of tissue sections and single cells.</a> The Journal of Neuroscience. 21, 8310-8314 (2001).</li><li>Van Gelder, R. N., von Zastrow, M. E., Yool, A., Dement, W. C., Barchas, J. D., Eberwine, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Amplified+RNA+synthesized+from+limited+quantities+of+heterogeneous+cDNA.">Amplified RNA synthesized from limited quantities of heterogeneous cDNA.</a> Proc. Natl. Acad. Sci. USA. 87, 1663-1667 (1990).</li><li>Miyashiro, K., Dichter, M., Eberwine, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+nature+and+differential+distribution+of+mRNAs+in+hippocampal+neuritis:+Implications+for+neuronal+functioning.">On the nature and differential distribution of mRNAs in hippocampal neuritis: Implications for neuronal functioning.</a> Proc. Natl. Acad. Sci. USA. 91, 10800-10804 (1994).</li><li>Sul, J., Wo, C. K., Zeng, F., Jochems, J., Lee, M. T., Kim, T. K., Peritz, T., Buckley, P., Cappelleri, D. J., Maronski, M., Kim, M., Kumar, V., Meaney, D., Kim, J., Eberwine, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcriptional+transfer+produces+a+predictable+cellular+phenotype.">Transcriptional transfer produces a predictable cellular phenotype.</a> Proc. Natl. Acad. Sci. USA. 106, 7624-7629 (2009).</li><li>Sow, F. B., Gallup, J. M., Sacco, R. E., Ackerman, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laser+capture+microdissection+revisited+as+a+tool+for+transcriptomic+analysis:+Application+of+an+excel-based+qPCR+preparation+software+(PREXCEL-Q).">Laser capture microdissection revisited as a tool for transcriptomic analysis: Application of an excel-based qPCR preparation software (PREXCEL-Q).</a> Int. J. Biomed. Sci. 5, (2010).</li><li>Vandewoestyne, M., Deforce, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laser+capture+microdissection+in+forensic+research:+a+review.">Laser capture microdissection in forensic research: a review.</a> Int J Legal Med. 124, (2010).</li><li>Eberwine, J., Bartfai, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+cell+transcriptomics+of+hypothalamic+warm+sensitive+neurons+that+control+core+body+temperature+and+fever+response+Signaling+asymmetry+and+an+extension+of+chemical+neuroanatomy.">Single cell transcriptomics of hypothalamic warm sensitive neurons that control core body temperature and fever response Signaling asymmetry and an extension of chemical neuroanatomy.</a> Pharmacol. Ther. , (2010).</li></ol>

Dr. Eberwine è un inventore sul brevetto ARNA che ha ottenuto la licenza per le tecnologie LBS in cui il Dr. Eberwine è un azionista.

Note e risoluzione dei problemi <ul><li> Si consiglia di assumere prima e dopo le immagini mostrano che la cellula bersaglio è stato isolato e che la penombra rimanente è stato lasciato intatto. </li><li> Se troppa soluzione sta entrando la pipetta come sei raccolta, è possibile utilizzare 3 vie Luer-Lock raccordi e lo stantuffo della siringa per tenere a pressione positiva nelle tubazioni. Il volume desiderato varia a seconda del tipo di lavorazione, ma fino a 5 microlitri dovrebbe andare bene per la maggior parte delle applicazioni. </li></ul> Consigli generali su tecniche di biologia molecolare <ul><li> Vortex tutti i tubi magazzino e spin giù prima di aggiungere ad una reazione. MAI enzimi vortice. </li><li> Mescolare bene le reazioni prima di aggiungere l&#39;enzima per garantire che il buffer è alla giusta concentrazione. </li><li> Mantenere le scorte di enzimi a -20 ° C se possibile usando un stratacooler. In caso contrario, rimuovere destra prima dell&#39;uso, tenere su ghiaccio, e tornare immediatamente a -20 ° C. </li><li> Sempre fare Master Mix quando si prepara più di una reazione per ridurre gli errori di pipettamento. Calcolare il volume richiesto in base al numero di campioni e aggiungere 10-20%. </li><li> Conservare l&#39;RNA a -80 ° C a ritardare il degrado. L&#39;RNA è più stabile memorizzati nel buffer per apurination ritardare di RNA che si verifica in condizioni di acidità. </li></ul> Schema generale della procedura ARNA Figura 4A illustra il primo round della procedura di Arna. Nella reazione primo filone, la poli-T porzione di T7-oligo (dT) primer seleziona per le specie di mRNA (lungo rettangolo bianco) legandosi alla coda polyA. Alcuni microRNA sono anche polyadenylated e saranno catturati da questa procedura. Ancora più importante, tuttavia, l&#39;RNA più abbondante nella cellula, RNA ribosomiale, no. Questo oligo funge da primer per trascrittasi inversa per sintetizzare un filamento complementare del cDNA (rettangolo grigio lungo) con l&#39;mRNA come modello. La parte del T7 T7-oligo (dT) primer incorpora il promotore T7 RNA polimerasi a telaio con la sequenza antisenso per l&#39;mRNA di partenza. Questo è utilizzato in seguito nella reazione di trascrizione in vitro. Successivamente, l&#39;mRNA in mRNA / DNA ibrido creato nel passaggio precedente è parzialmente idrolizzato dalla RNasi H creando RNA &quot;primer&quot; (piccoli rettangoli bianchi) simile ai frammenti di Okazaki creato nella sintesi del filamento di DNA in ritardo di sviluppo. DNA polimerasi I utilizza frammenti di RNA di sintesi del DNA primi utilizzando il DNA complementare al mRNA come modello. Quando raggiunge il frammento successivo RNA, i suoi 5 &#39;a 3&#39; nucleasica rimuove il ribonucleotidi e li sostituisce con deossiribonucleotidi. La DNA ligasi è aggiunto a legare ogni filoni in cui la sostituzione del filo guida non è completa. DNA polimerasi T4 è aggiunta per riempire nelle zone in cui frammenti di RNA servito come primer iniziale per la DNA polimerasi I creando un blunt-ended a doppio filamento cDNA che viene poi purificato prima di effettuare la reazione IVT. Nella reazione IVT, T7 RNA polimerasi si lega al promotore T7 incorporato nella doppia elica del DNA e sintetizza le molecole di RNA antisenso (lunghi rettangoli neri) con il senso del filo come modello. Questo serve come il passo di amplificazione in cui si producono migliaia di molecole di RNA antisenso da ogni molecola doppio filamento del DNA (Figura 4A). Il secondo turno, come illustrato nella figura 4B, inizia con una reazione di trascrizione inversa che è leggermente diverso da quello del primo turno dato che di partenza è l&#39;RNA antisenso (solido rettangolo nero) e manca la coda polyadenylated che è stato interessato dagli T7-oligo (dT) primer al primo turno. Pertanto, questa reazione è innescata con primer random (piccoli rettangoli grigi) e successivamente denaturato RNA. La reazione secondo filone è poi innescata dalla T7-oligo (dT) primer, che si lega alla poli-Una sequenza all&#39;estremità 3 &#39;dell&#39;RNA senso creati nella reazione precedente trascrizione inversa. Un&#39;altra reazione IVT viene eseguita nello stesso modo come nel primo turno. Il secondo turno è di solito ripetuta almeno una volta per raggiungere tre turni di amplificazione da una singola cellula. Applicazioni Le tecniche che abbiamo presentato in questo articolo può essere tradotto in un gran numero di applicazioni. Il singolo protocollo di isolamento delle cellule possono essere modificati per essere utilizzati in fette acuta. 14 Anche se tecnicamente più impegnativi, gli stessi principi si applicano in questa preparazione alternativa. Inoltre, se la dimensione della pipetta è leggermente adattato, registrazioni della fisiologia delle cellule può essere fatta prima della raccolta consentendo una ben controllata studio dei meccanismi molecolari alla base uscite fisiologiche. Un&#39;altra piccola modifica è quello di isolare i processi dal soma cellulare. 15 Per questa applicazione, raccogliere corpi cellulari con una pipetta e poi tornare con una pipetta fresca e raccogliere 100-300 dendrit identificatoes o assoni al tubo di raccolta 16. Una volta che le cellule sono state raccolte, i confronti di abbondanze mRNA e composizioni può essere fatta tra diverse e anche all&#39;interno della popolazione stessa cella. Incorporando biotinilato-UTP nel ARNA terzo turno per l&#39;analisi dei microarray permette di determinare questi mRNA abbondanze relative. La composizione della popolazione mRNA originale può essere determinata anche dopo la procedura ARNA utilizzando sequenziamento di nuova generazione. L&#39;ARNA amplificato può essere utilizzato anche per confermare il fenotipo delle cellule studi di conversione in cui vengono transfettate una serie completa degli mRNA da un tipo di cellula in un tipo cellulare diverso al fine di indurre transizione del fenotipo del tipo di cellula quest&#39;ultima in quella dei primi, una procedura sviluppata dal laboratorio e conosciuto come Tiper. 17 Questi studi sono particolarmente utili per lo studio di stati di malattia e fenotipi cellulari e tali studi sono attualmente in corso in laboratorio. RT-PCR o qPCR può essere eseguita sul materiale amplificato per confermare l&#39;espressione di specifici geni delle cellule. Inoltre, le valutazioni di efficienza di trasfezione o trasduzione può essere fatta a livello di singola cellula. Vantaggi e limiti Come affermato in astratto, l&#39;isolamento di singole cellule per l&#39;analisi elimina gli effetti media visto con l&#39;analisi di popolazioni cellulari eterogenee. Questi effetti media travisare abbondanze mRNA all&#39;interno di una singola cellula da un eccesso di rappresentanza trascrizioni abbondante e mediazione e la prevenzione di molte rilevamento a basso abbondanza trascrizioni. Citometria a flusso può essere utilizzato per ordinare le singole cellule, ma questo metodo richiede la conoscenza di marcatori specifici delle cellule e costose attrezzature. 18 microdissezione catturare laser sia con sistemi di acquisizione IR o UV microdissezione laser permettono di singola cellula e perfino catturare subcellulare, ma richiede cellule di interesse per essere situati sulla superficie delle sezioni molto sottili. 19 Simile alla citometria a flusso, microdissezione laser capture richiede costose attrezzature. Uno dei principali vantaggi della tecnica di base collezione elettrodo sopra descritti è che importanti dati elettrofisiologici possono essere ottenute dalla cella di interesse prima del raccolto, permettendo l&#39;analisi funzionale del trascrittoma e da eseguire sulla cella stessa. 20 A lato negativo della nostra tecnica è che richiede esperienza nell&#39;uso di micromanipolatori. Gli investigatori familiarità con micromanipolatori troveranno questa tecnica molto intuitivo, tuttavia, gli individui con nessuna esperienza quali sarà necessario per familiarizzare con i movimenti fini necessari. Inerenti a qualsiasi tecnica di amplificazione è l&#39;amplificazione preferenziale di alcune trascrizioni in base alle dimensioni e alla composizione dei nucleotidi. 4,6,7 reazione a catena della polimerasi (PCR), tecniche di base come reverse-trascrizione reazione a catena della polimerasi (RT-PCR) e la rapida amplificazione di cDNA estremità (RACE) comportano l&#39;amplificazione esponenziale di trascrizioni, mentre l&#39;ARNA procedura di amplificazione risultati di amplificazione lineare. Così, uno dei principali vantaggi della procedura ARNA risiede nella sua capacità di preservare meglio l&#39;abbondanza relativa di mRNA trascritti da solo linearmente amplificando eventuali errori o distorsioni che si verificano nel processo di amplificazione al contrario di amplificare esponenzialmente detto errori e pregiudizi. La procedura ARNA accoppiata con analisi microarray permette la comparazione delle abbondanze mRNA tra singole cellule di morfologia simili o differenti, trattati o non trattati. Inoltre, il materiale amplificato possono essere presentate per il sequenziamento di nuova generazione. 5,8 Tuttavia, occorre prestare attenzione a queste analisi in quanto, in contrasto con l&#39;uso di primer a caso per la procedura, l&#39;oligo-dT primer procedura sopra descritta amplificazione pregiudizi del 3 &#39;estremità del mRNA e in genere si traduce in un accorciamento leggera successive materiale amplificato con ogni turno. Si deve prestare attenzione nel valutare i risultati dei microarray con metodi standard come alcune false chiamate assenti possono derivare da un po &#39;accorciato materiale amplificato. Inoltre, i risultati mentre sequenziamento sarà davvero fornirà la piena 5 &#39;sequenza della maggior parte degli mRNA originale, il 5&#39; sequenze di alcuni mRNA possono perdere. Per queste ragioni, il numero di giri di amplificazioni dovrebbe essere limitato.

A correction was made to <a href="http://http://www.jove.com/video/2634/transcriptome-analysis-of-single-cells">Transcriptome Analysis of Single Cells</a>. There were errors in the volumes used in the aRNA Amplification section.

Erratum: Transcriptome Analysis of Single Cells

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">	
		
		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>Spiegelgas coverslips</td>
<td>&nbsp;</td>
<td>Carolina Biological</td>
<td>63-3029</td>
<td>&nbsp;</td>
<tr>
<td>Nunc 35x10 mm culture dishes</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>12-565-90</td>
<td>&nbsp;</td>
<tr>
<td>Water for cell culture</td>
<td>&nbsp;</td>
<td>Lonza</td>
<td>17-724Q</td>
<td>For making solutions used for cell culture and rinsing coverslips</td>
</tr>
<tr>
<td>Poly-D-Lysine MW70-150K</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>6407</td>
<td>&nbsp;</td>
<tr>
<td>Laminin, ultrapure</td>
<td>&nbsp;</td>
<td>BD Bioscience</td>
<td>354239</td>
<td>&nbsp;</td>
<tr>
<td>Boric acid</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>B0252</td>
<td>&nbsp;</td>
<tr>
<td>MEM with Earle&#x2019;s salts and glutamax</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>41090-101</td>
<td>For plating cells</td>
</tr>
<tr>
<td>D-glucose</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>G8769</td>
<td>&nbsp;</td>
<tr>
<td>Penicillin-streptomycin</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>15140-122</td>
<td>&nbsp;</td>
<tr>
<td>Horse serum</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>16050</td>
<td>&nbsp;</td>
<tr>
<td>Cytosine beta-D-arabinofuranoside</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>C1768</td>
<td>&nbsp;</td>
<tr>
<td>MEM with Earle&#x2019;s salts and L-glutamine</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>11095-098</td>
<td>For growing cells</td>
</tr>
<tr>
<td>Sodium pyruvate</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>P2256</td>
<td>&nbsp;</td>
<tr>
<td>B27 serum-free supplement</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>17504-044</td>
<td>&nbsp;</td>
<tr>
<td>Borosilicate glass capillary tubes (1.5mm O.D, 100mm length)</td>
<td>&nbsp;</td>
<td>Kimble Chase</td>
<td>34500 99</td>
<td>Any borosilicate glass pipette will work as long as the proper bore size is attained. </td>
</tr>
<tr>
<td>HBSS</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>14175</td>
<td>Any solution will work as long as the components won&#x2019;t interfere with any future processing (i.e. no Ca2+ or Mg2+)</td>
</tr>
<tr>
<td>1ml syringe</td>
<td>&nbsp;</td>
<td>BD</td>
<td>309628</td>
<td>&nbsp;</td>
<tr>
<td>Needle</td>
<td>&nbsp;</td>
<td>BD</td>
<td>&nbsp;</td>
<td>Gauge depends on the diameter of the pipettes</td>
</tr>
<tr>
<td>dNTP mix</td>
<td>&nbsp;</td>
<td>Amersham</td>
<td>28-4065-51</td>
<td>&nbsp;</td>
<tr>
<td>dt-T7 oligo</td>
<td>&nbsp;</td>
<td>Custom</td>
<td>Midland Certified</td>
<td>&nbsp;</td>
<tr>
<td>Second strand buffer (5x)</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>Y01129</td>
<td>&nbsp;</td>
<tr>
<td>DTT</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>Supplied with second strand buffer</td>
</tr>
<tr>
<td>E.coli DNA Ligase</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>100002324</td>
<td>&nbsp;</td>
<tr>
<td>DNA polymerase I</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>100004926</td>
<td>&nbsp;</td>
<tr>
<td>Rnase H</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>18021-071</td>
<td>&nbsp;</td>
<tr>
<td>Megascript T7 kit</td>
<td>&nbsp;</td>
<td>Ambion</td>
<td>AM1334</td>
<td>&nbsp;</td>
<tr>
<td>Random primers</td>
<td>&nbsp;</td>
<td>BMB</td>
<td>11034731001</td>
<td>&nbsp;</td>
<tr>
<td>Superscript III Reverse Transcriptase</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>56575</td>
<td>in kit (18080-044) comes with first strand buffer (Y02321) and DTT</td>
</tr>
<tr>
<td>MEGAclear Kit</td>
<td>&nbsp;</td>
<td>Ambion</td>
<td>1908</td>
<td>&nbsp;</td>
<tr>
<td>MinElute Reaction Cleanup Kit</td>
<td>&nbsp;</td>
<td>Qiagen</td>
<td>28206</td>
<td>&nbsp;</td>
<tr>
<td>T4 DNA polymerase</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>100004994</td>
<td>&nbsp;</td>
<tr>
<td>Rnasin</td>
<td>&nbsp;</td>
<td>Promega</td>
<td>N251B</td>
<td>&nbsp;</td>
<tr>
<td>Illumina TotalPrep RNA Amplification Kit</td>
<td>&nbsp;</td>
<td>Ambion</td>
<td>AMIL1791</td>
<td>&nbsp;</td>
<tr>
<td>Flaming/Brown micropipette puller</td>
<td>&nbsp;</td>
<td>Sutter Instruments</td>
<td>P-87</td>
<td>Sutter has many other models, many are discussed in the cookbook</td>
</tr>
<tr>
<td>Micromanipulator</td>
<td>&nbsp;</td>
<td>Olympus</td>
<td>&nbsp;</td>
<td>Many other micromanipulators will work such as the newer Eppendorf models</td>
</tr>
<tr>
<td>Pipette Holder</td>
<td>&nbsp;</td>
<td>Warner Instruments</td>
<td>MP-S15A</td>
<td>Will vary with micromanipulator and pipette O.D.</td>
</tr>
<tr>
<td>Bioanalyzer RNA 6000 Nano Kit</td>
<td>&nbsp;</td>
<td>Agilent</td>
<td>5067-1511</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>

transcriptome analysis of single cells

Molte tecniche di analisi di espressione genica si basano su materiale isolato da popolazioni eterogenee di cellule da omogenati di tessuti o cellule in coltura. 1,2,3 Nel caso del cervello, regioni come l&#39;ippocampo contiene una disposizione complessa di diversi tipi di cellule, ciascuna con profili di mRNA distinte. La capacità di raccogliere le singole cellule consente una più approfondita indagine sulle differenze molecolari tra e all&#39;interno di popolazioni cellulari. Descriviamo un metodo semplice e rapido per la raccolta delle cellule per ulteriori elaborazioni. Pipette spesso usato in elettrofisiologia sono utilizzati per isolare (con aspirazione) una cella di interesse e convenientemente lo depositano in una provetta Eppendorf per l&#39;ulteriore elaborazione con qualsiasi numero di tecniche di biologia molecolare. Il nostro protocollo può essere modificato per la raccolta dei dendriti da colture cellulari o anche singole cellule da fette acuta. Abbiamo anche descrivere il metodo di amplificazione ARNA come applicazione principale a valle di isolamenti singola cellula. Questo metodo è stato sviluppato in precedenza dal nostro laboratorio come alternativa alle altre tecniche di analisi dell&#39;espressione genica come reverse-trascrizione o real-time polymerase chain reaction (PCR). 4,5,6,7,8 Questa tecnica prevede l&#39;amplificazione lineare dei polyadenylated RNA a partire femtogrammi solo del materiale e conseguente quantità microgrammo di RNA antisenso. Il materiale linearmente amplificato fornisce una più accurata stima di amplificazione esponenziale della relativa abbondanza di componenti del trascrittoma delle cellule isolate. La procedura di base consiste in due turni di amplificazione. In breve, un RNA polimerasi di T7 sito promotore è incorporata nel doppio filamento del DNA creati dal verbale mRNA. Una notte nella trascrizione in vitro (IVT) di reazione viene quindi eseguita in cui T7 RNA polimerasi produce molte trascrizioni antisenso dal cDNA a doppio filamento. Il secondo turno si ripete questo processo, ma con alcune differenze tecniche, poiché il materiale di partenza è l&#39;RNA antisenso. E &#39;normale ripetere il secondo turno, con conseguente tre turni di amplificazione. Spesso, il terzo turno in reazione trascrizione in vitro viene eseguita utilizzando nucleosidi trifosfati biotinilato in modo che il RNA antisenso prodotta può essere ibridato e rilevato su un microarray. 7,8

Watch this Scientific Journal Video about Transcriptome Analysis of Single Cells at JoVE.com

Transcriptome Analysis of Single Cells

In questo articolo viene descritto un metodo semplice per la raccolta di singole cellule di ratto colture primarie neuronali e analisi del trascrittoma con conseguente amplificazione ARNA. Questo approccio è generalizzabile a qualsiasi tipo di cellula.

L&#39;analisi del trascrittoma di singole cellule

Many gene expression analysis techniques rely on material isolated from heterogeneous populations of cells from tissue homogenates or cells in ...

Research

JoVE Journal

Neuroscience

29.6K Views.  University of Pennsylvania. In questo articolo viene descritto un metodo semplice per la raccolta di singole cellule di ratto colture primarie neuronali e analisi del trascrittoma con conseguente amplificazione ARNA. Questo approccio è generalizzabile a qualsiasi tipo di cellula.

Video: Transcriptome Analysis of Single Cells

Live-cell Imaging of Sensory Organ Precursor Cells in Intact Drosophila Pupae

Since the discovery of Green Fluorescent Protein (GFP), there has been a revolutionary change in the use of live-cell imaging as a tool for understanding fundamental biological mechanisms. Striking progress has been particularly evident in Drosophila, whose extensive toolkit of mutants and transgenic lines provides a convenient model to study evolutionarily-conserved developmental and cell biological mechanisms. We are interested in understanding the mechanisms that control cell fate specification in the adult peripheral nervous system (PNS) in Drosophila. Bristles that cover the head, thorax, abdomen, legs and wings of the adult fly are individual mechanosensory organs, and have been studied as a model system for understanding mechanisms of Notch-dependent cell fate decisions. Sensory organ precursor (SOP) cells of the microchaetes (or small bristles), are distributed throughout the epithelium of the pupal thorax, and are specified during the first 12 hours after the onset of pupariation. After specification, the SOP cells begin to divide, segregating the cell fate determinant Numb to one daughter cell during mitosis. Numb functions as a cell-autonomous inhibitor of the Notch signaling pathway.
Here, we show a method to follow protein dynamics in SOP cell and its progeny within the intact pupal thorax using a combination of tissue-specific Gal4 drivers and GFP-tagged fusion proteins 1,2.This technique has the advantage over fixed tissue or cultured explants because it allows us to follow the entire development of an organ from specification of the neural precursor to growth and terminal differentiation of the organ. We can therefore directly correlate changes in cell behavior to changes in terminal differentiation. Moreover, we can combine the live imaging technique with mosaic analysis with a repressible cell marker (MARCM) system to assess the dynamics of tagged proteins in mitotic SOPs under mutant or wildtype conditions. Using this technique, we and others have revealed novel insights into regulation of asymmetric cell division and the control of Notch signaling activation in SOP cells (examples include references 1-6,7 ,8).

Live-cell Imaging of Sensory Organ Precursor Cells in Intact Drosophila Pupae

In this video, we describe a method for live cell imaging of asymmetrically dividing sensory organ progenitor cells and epidermal cells in intact Drosophila pupae

Live-cellula Imaging di cellule sensoriali Precursore in Organo intatto Drosophila Pupae

Since the discovery of Green Fluorescent Protein (GFP), there has been a revolutionary change in the use of live-cell imaging as a tool for understanding ...

Ricerca

Neuroscienze

Sequential Photo-bleaching to Delineate Single Schwann Cells at the Neuromuscular Junction

Sequential photo-bleaching provides a non-invasive way to label individual SCs at the NMJ. The NMJ is the largest synapse of the mammalian nervous system and has served as guiding model to study synaptic structure and function. In mouse NMJs motor axon terminals form pretzel-like contact sites with muscle fibers. The motor axon and its terminal are sheathed by SCs. Over the past decades, several transgenic mice have been generated to visualize motor neurons and SCs, for example Thy1-XFP1 and Plp-GFP mice2, respectively.
Along motor axons, myelinating axonal SCs are arranged in non-overlapping internodes, separated by nodes of Ranvier, to enable saltatory action potential propagation. In contrast, terminal SCs at the synapse are specialized glial cells, which monitor and promote neurotransmission, digest debris and guide regenerating axons. NMJs are tightly covered by up to half a dozen non-myelinating terminal SCs - these, however, cannot be individually resolved by light microscopy, as they are in direct membrane contact3.
Several approaches exist to individually visualize terminal SCs. None of these are flawless, though. For instance, dye filling, where single cells are impaled with a dye-filled microelectrode, requires destroying a labelled cell before filling a second one. This is not compatible with subsequent time-lapse recordings3. Multi-spectral "Brainbow" labeling of SCs has been achieved by using combinatorial expression of fluorescent proteins4. However, this technique requires combining several transgenes and is limited by the expression pattern of the promoters used. In the future, expression of "photo-switchable" proteins in SCs might be yet another alternative5. Here we present sequential photo-bleaching, where single cells are bleached, and their image obtained by subtraction. We believe that this approach - due to its ease and versatility - represents a lasting addition to the neuroscientist's technology palette, especially as it can be used in vivo and transferred to others cell types, anatomical sites or species6.
In the following protocol, we detail the application of sequential bleaching and subsequent confocal time-lapse microscopy to terminal SCs in triangularis sterni muscle explants. This thin, superficial and easily dissected nerve-muscle preparation7,8 has proven useful for studies of NMJ development, physiology and pathology9. Finally, we explain how the triangularis sterni muscle is prepared after fixation to perform correlated high-resolution confocal imaging, immunohistochemistry or ultrastructural examinations.

Visualizing individual cells in densely packed tissues, such as terminal Schwann cells (SCs) at neuromuscular junctions (NMJs), is challenging. "Sequential photo-bleaching" allows delineating single terminal SCs, for instance in the triangularis sterni muscle explant, a convenient nerve-muscle preparation, where sequential bleaching can be combined with time-lapse imaging and post-hoc immunostainings.

Sequential Photo-sbiancante per Delineare cellule di Schwann singoli sulla giunzione neuromuscolare

Sequential photo-bleaching provides a non-invasive way to label individual SCs at the NMJ. The NMJ is the largest synapse of the mammalian nervous system ...

Labeling of Single Cells in the Central Nervous System of Drosophila melanogaster

In this article we describe how to individually label neurons in the embryonic CNS of Drosophila melanogaster by juxtacellular injection of the lipophilic fluorescent membrane marker DiI. This method allows the visualization of neuronal cell morphology in great detail. It is possible to label any cell in the CNS: cell bodies of target neurons are visualized under DIC optics or by expression of a fluorescent genetic marker such as GFP. After labeling, the DiI can be transformed into a permanent brown stain by photoconversion to allow visualization of cell morphology with transmitted light and DIC optics. Alternatively, the DiI-labeled cells can be observed directly with confocal microscopy, enabling genetically introduced fluorescent reporter proteins to be colocalised. The technique can be used in any animal, irrespective of genotype, making it possible to analyze mutant phenotypes at single cell resolution.

Labeling of Single Cells in the Central Nervous System of Drosophila melanogaster

We present a technique for labeling single neurons in the central nervous system (CNS) of Drosophila embryos, which allows the analysis of neuronal morphology by either transmitted light or confocal microscopy.

Etichettatura di singole cellule nel sistema nervoso centrale di<em&gt; Drosophila melanogaster</em

In this  article we describe how to individually label neurons in the embryonic CNS of Drosophila melanogaster by juxtacellular injection of the ...

Laser Capture Microdissection of Enriched Populations of Neurons or Single Neurons for Gene Expression Analysis After Traumatic Brain Injury

Long-term cognitive disability after TBI is associated with injury-induced neurodegeneration in the hippocampus-a region in the medial temporal lobe that is critical for learning, memory and executive function.1,2 Hence our studies focus on gene expression analysis of specific neuronal populations in distinct subregions of the hippocampus. The technique of laser capture microdissection (LCM), introduced in 1996 by Emmert-Buck, et al.,3 has allowed for significant advances in gene expression analysis of single cells and enriched populations of cells from heterogeneous tissues such as the mammalian brain that contains thousands of functional cell types.4 We use LCM and a well established rat model of traumatic brain injury (TBI) to investigate the molecular mechanisms that underlie the pathogenesis of TBI. Following fluid-percussion TBI, brains are removed at pre-determined times post-injury, immediately frozen on dry ice, and prepared for sectioning in a cryostat. The rat brains can be embedded in OCT and sectioned immediately, or stored several months at -80 &deg;C before sectioning for laser capture microdissection. Additionally, we use LCM to study the effects of TBI on circadian rhythms. For this, we capture neurons from the suprachiasmatic nuclei that contain the master clock of the mammalian brain. Here, we demonstrate the use of LCM to obtain single identified neurons (injured and degenerating, Fluoro-Jade-positive, or uninjured, Fluoro-Jade-negative) and enriched populations of hippocampal neurons for subsequent gene expression analysis by real time PCR and/or whole-genome microarrays. These LCM-enabled studies have revealed that the selective vulnerability of anatomically distinct regions of the rat hippocampus are reflected in the different gene expression profiles of different populations of neurons obtained by LCM from these distinct regions. The results from our single-cell studies, where we compare the transcriptional profiles of dying and adjacent surviving hippocampal neurons, suggest the existence of a cell survival rheostat that regulates cell death and survival after TBI.

We describe how to use laser capture microdissection (LCM) to obtain enriched populations of hippocampal neurons or single neurons from frozen sections of the injured rat brain for subsequent gene expression analysis using quantitative real time PCR and/or whole-genome microarrays.

Laser Microdissezione Cattura di popolazioni Arricchito di neuroni singoli neuroni o per analisi di espressione genica dopo trauma cranico

Long-term cognitive disability after TBI is associated with injury-induced neurodegeneration in the hippocampus-a region in the medial temporal lobe that ...

Peering at Brain Polysomes with Atomic Force Microscopy

The translational machinery, i.e., the polysome or polyribosome, is one of the biggest and most complex cytoplasmic machineries in cells. Polysomes, formed by ribosomes, mRNAs, several proteins and non-coding RNAs, represent integrated platforms where translational controls take place. However, while the ribosome has been widely studied, the organization of polysomes is still lacking comprehensive understanding. Thus much effort is required in order to elucidate polysome organization and any novel mechanism of translational control that may be embedded. Atomic force microscopy (AFM) is a type of scanning probe microscopy that allows the acquisition of 3D images at nanoscale resolution. Compared to electron microscopy (EM) techniques, one of the main advantages of AFM is that it can acquire thousands of images both in air and in solution, enabling the sample to be maintained under near physiological conditions without any need for staining and fixing procedures. Here, a detailed protocol for the accurate purification of polysomes from mouse brain and their deposition on mica substrates is described. This protocol enables polysome imaging in air and liquid with AFM and their reconstruction as three-dimensional objects. Complementary to cryo-electron microscopy (cryo-EM), the proposed method can be conveniently used for systematically analyzing polysomes and studying their organization.

While ribosome structure has been extensively characterized, the organization of polysomes is still understudied. To overcome this lack of knowledge, we present here a detailed preparation protocol for accurate imaging of mammalian polysomes by atomic force microscopy (AFM) in air and liquid.

Scrutando Cervello polisomi con microscopia a forza atomica

The translational machinery, i.e., the polysome or polyribosome, is one of the biggest and most complex cytoplasmic machineries in cells. Polysomes, ...

Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells

The discovery of cell type-specific markers can provide insight into cellular function and the origins of cellular heterogeneity. With a recent push for the improved understanding of neuronal diversity, it is important to identify genes whose expression defines various subpopulations of cells. The retina serves as an excellent model for the study of central nervous system diversity, as it is composed of multiple major cell types. The study of each major class of cells has yielded genetic markers that facilitate the identification of these populations. However, multiple subtypes of cells exist within each of these major retinal cell classes, and few of these subtypes have known genetic markers, although many have been characterized by morphology or function. A knowledge of genetic markers for individual retinal subtypes would allow for the study and mapping of brain targets related to specific visual functions and may also lend insight into the gene networks that maintain cellular diversity. Current avenues used to identify the genetic markers of subtypes possess drawbacks, such as the classification of cell types following sequencing. This presents a challenge for data analysis and requires rigorous validation methods to ensure that clusters contain cells of the same function. We propose a technique for identifying the morphology and functionality of a cell prior to isolation and sequencing, which will allow for the easier identification of subtype-specific markers. This technique may be extended to non-neuronal cell types, as well as to rare populations of cells with minor variations. This protocol yields excellent-quality data, as many of the libraries have provided read depths greater than 20 million reads for single cells. This methodology overcomes many of the hurdles presented by Single-cell RNA-Seq and may be suitable for researchers aiming to profile cell types in a straightforward and highly efficient manner.

Here, we present a combinatorial approach for classifying neuronal cell types prior to isolation and for the subsequent characterization of single-cell transcriptomes. This protocol optimizes the preparation of samples for successful RNA Sequencing (RNA-Seq) and describes a methodology designed specifically for the enhanced understanding of cellular diversity.

Sequenza RNA a singola cellula di sottogruppi definiti delle cellule del Ganglio retinico

The discovery of cell type-specific markers can provide insight into cellular function and the origins of cellular heterogeneity. With a recent push for ...

Analysis of Immune Cells in Single Sciatic Nerves and Dorsal Root Ganglion from a Single Mouse Using Flow Cytometry

Nerve-resident immune cells in the peripheral nervous system (PNS) are essential to maintaining neuronal integrity in a healthy nerve. The immune cells of the PNS are affected by injury and disease, affecting the nerve function and the capacity for regeneration. Neuronal immune cells are commonly analyzed by immunofluorescence (IF). While IF is essential for determining the location of the immune cells in the nerve, IF is only semi-quantitative and the method is limited to the number of markers that can be analyzed simultaneously and the degree of surface expression. In this study, flow cytometry was used for quantitative analysis of leukocyte infiltration into sciatic nerves or dorsal root ganglions (DRGs) of individual mice. Single cell analysis was performed using DAPI and several proteins were analyzed simultaneously for either surface or intracellular expression. Both sciatic nerves from one mouse that were treated according to this protocol generated &#8805; 30,000 single nucleated events. The proportion of leukocytes in the sciatic nerves, determined by expression of CD45, was approximately 5% of total cell content in the sciatic nerve and approximately 5-10% in the DRG. Although this protocol focuses primarily on the immune cell population within the PNS, the flexibility of flow cytometry to measure a number of markers simultaneously means that the other cells populations present within the nerve, such as Schwann cells, pericytes, fibroblasts, and endothelial cells, can also be analyzed using this method. This method therefore provides a new means for studying systemic effects on the PNS, such as neurotoxicology and genetic models of neuropathy or in chronic diseases, such as diabetes.

Quantitative analysis of cell content within the murine sciatic nerve is difficult due to the scarcity of the tissue. This protocol describes a method for tissue digestion and preparation that provides sufficient cells for flow cytometry analysis of immune cell populations from nerves of individual mice.

Analisi delle cellule immuni in singolo nervo sciatico e del ganglio della radice dorsale da un singolo Mouse mediante citometria a flusso

Nerve-resident immune cells in the peripheral nervous system (PNS) are essential to maintaining neuronal integrity in a healthy nerve. The immune cells of ...

Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing

Probing an individual cell&#39;s gene expression enables the identification of cell type and cell state. Single-cell RNA sequencing has emerged as a powerful tool for studying transcriptional profiles of cells, particularly in heterogeneous tissues such as the central nervous system. However, dissociation methods required for single cell sequencing can lead to experimental changes in the gene expression and cell death. Furthermore, these methods are generally restricted to fresh tissue, thus limiting studies on archival and bio-bank material. Single nucleus RNA sequencing (snRNA-Seq) is an appealing alternative for transcriptional studies, given that it accurately identifies cell types, permits the study of tissue that is frozen or difficult to dissociate, and reduces dissociation-induced transcription. Here, we present a high-throughput protocol for rapid isolation of nuclei for downstream snRNA-Seq. This method enables isolation of nuclei from fresh or frozen spinal cord samples and can be combined with two massively parallel droplet encapsulation platforms.

Here, we present a protocol to rapidly isolate high-quality nuclei from the fresh or frozen tissue for downstream massively parallel RNA sequencing. We include detergent-mechanical and hypotonic-mechanical tissue disruption and cell lysis options, both of which can be used for isolation of nuclei.

Isolamento dei Nuclei del midollo spinale adulto per il sequenziamento massivamente parallelo Single-nucleo RNA

Probing an individual cell&#39;s gene expression enables the identification of cell type and cell state. Single-cell RNA sequencing has emerged as a ...

Analysis of Spliceosomal snRNA Localization in Human Hela Cells Using Microinjection

Biogenesis of spliceosomal snRNAs is a complex process involving both nuclear and cytoplasmic phases and the last step occurs in a nuclear compartment called the Cajal body. However, sequences that direct snRNA localization into this subnuclear structure have not been known until recently. To determine sequences important for accumulation of snRNAs in Cajal bodies, we employed microinjection of fluorescently labelled snRNAs followed by their localization inside cells. First, we prepared snRNA deletion mutants, synthesized DNA templates for in vitro transcription and transcribed snRNAs in the presence of UTP coupled with Alexa488. Labelled snRNAs were mixed with 70 kDa-Dextran conjugated with TRITC, and microinjected to the nucleus or the cytoplasm of human HeLa cells. Cells were incubated for 1 h and fixed and the Cajal body marker coilin was visualized by indirect immunofluorescence, while snRNAs and dextran, which serves as a marker of nuclear or cytoplasmic injection, were observed directly using a fluorescence microscope. This method allows for efficient and rapid testing of how various sequences influence RNA localization inside cells. Here, we show the importance of the Sm-binding sequence for efficient localization of snRNAs into the Cajal body.

Biogenesis of spliceosomal snRNAs is a complex process involving various cellular compartments. Here, we employed microinjection of fluorescently labelled snRNAs in order to monitor their transport inside the cell.

Analisi della localizzazione snRNA Spliceosomic nelle cellule umane di Hela utilizzando la microiniezione

Biogenesis of spliceosomal snRNAs is a complex process involving both nuclear and cytoplasmic phases and the last step occurs in a nuclear compartment ...

A Scalable Model to Study the Effects of Blunt-Force Injury in Adult Zebrafish

Blunt-force traumatic brain injuries (TBI) are the most common form of head trauma, which spans a range of severities and results in complex and heterogenous secondary effects. While there is no mechanism to replace or regenerate the lost neurons following a TBI in humans, zebrafish possess the ability to regenerate neurons throughout their body, including the brain. To examine the breadth of pathologies exhibited in zebrafish following a blunt-force TBI and to study the mechanisms underlying the subsequent neuronal regenerative response, we modified the commonly used rodent Marmarou weight drop for the use in adult zebrafish. Our simple blunt-force TBI model is scalable, inducing a mild, moderate, or severe TBI, and recapitulates many of the phenotypes observed following human TBI, such as contact- and post-traumatic seizures, edema, subdural and intracerebral hematomas, and cognitive impairments, each displayed in an injury severity-dependent manner. TBI sequelae, which begin to appear within minutes of the injury, subside and return to near undamaged control levels within 7 days post-injury. The regenerative process begins as early as 48 hours post-injury (hpi), with the peak cell proliferation observed by 60 hpi. Thus, our zebrafish blunt-force TBI model produces characteristic primary and secondary injury TBI pathologies similar to human TBI, which allows for investigating disease onset and progression, along with the mechanisms of neuronal regeneration that is unique to zebrafish.

We modified the Marmarou weight drop model for adult zebrafish to examine a breadth of pathologies following blunt-force traumatic brain injury (TBI) and the mechanisms underlying subsequent neuronal regeneration. This blunt-force TBI model is scalable, induces a mild, moderate, or severe TBI, and recapitulates injury heterogeneity observed in human TBI.