Name: single-cell rna-seq of defined subsets of retinal ganglion cells
Uploaded: 2017-05-22T12:30:00
Description: Watch this Scientific Journal Video about Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells at JoVE.com

Мы хотели бы выразить благодарность Дженнифер Баир и Эйнату Снир, а также Институту Генетики Университета Айовы за их помощь в подготовке и обработке образцов.

Все процедуры были одобрены Институциональным комитетом по уходу за животными и их использованием (IACUC) в Северо-западном университете. 1. Подготовка растворов для электрофизиологии (4 ч) <ol><li> Сделайте 0,1% DEPC-обработанной H 2 O добавлением 1 мл диэтилпирокарбоната (DEPC...

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Наш протокол демонстрирует с помощью быстрого и простого в использовании руководства метод подготовки отдельных клеток определенных морфологических классов для высококачественного секвенирования с небольшим ущербом для образца. В настоящей рукописи, собственно фоточувствительны?...

Разнообразие нейронов наблюдается во всей центральной нервной системе, особенно в сетчатке позвоночных, высокоспециализированной ткани, состоящей из 1 глиального и 6 типов нейронов, которые возникают из одной популяции клеток-предшественников сетчатки 1 , 2 , 3 . Многие подтипы клеток могут быть классифицированы функционально, морфологически и генетически. Цель этого протокола - связать генетическую изменчивость типов клеток с их идентифицируемыми функциональными и / или морфологическими характеристиками. Для классификации клеток было идентифицировано несколько генов, но многие подтипы продолжают оставаться нехарактеризованными, так как они представляют небольшую часть общей популяции. Идентификация генов в этих специфических подтипах позволит лучше понять разнообразие нейронов в сетчатке и может также пролить свет на диверсификацию нервных клеток в других местах. марихуанаБолее того, одноклеточные исследования позволяют выявлять новые типы клеток, которые, возможно, были упущены из-за их низкой представленности среди всего населения 4 , 5 , 6 , 7 . Одно из преимуществ одноклеточной транскриптомии заключается в том, что можно обнаружить уникальные маркеры или комбинации маркеров, которые определяют конкретный клеточный подтип. Затем они могут быть использованы для получения генетического доступа к этому типу клеток для различных манипуляций. Например, мы используем этот протокол, чтобы охарактеризовать гены определенного типа клеток подмножества клеток сетчатки ганглия, которые экспрессируют фотопигмент меланопсин. Использование флуоресцентного маркера в меланопсин-экспрессирующих ганглиозных клетках сетчатки позволяет исследовать эти клетки, поскольку они сгруппированы вместе из-за их экспрессии известного гена. Интересно, что существует пять известных подтипов этой ячейки popuВ сетчатке мыши 8 . Таким образом, для выделения РНК из клеток каждого типа мы использовали установленные морфологические классификации в трансгенной модели для идентификации каждого подтипа до выделения клеток. Этот метод позволяет характеризовать клетки, а также их выделение непосредственно из сетчатки, без необходимости диссоциации тканей, что может вызвать стресс-реакцию внутри клеток и загрязнение из-за разъединенных дендритов 9 . За последние несколько лет появилось множество новых методов, поскольку метод РНК-Seq продолжает развиваться. Эти инструменты позволяют добиться максимальной мобильности клеток и большей эффективности затрат при приближении к вопросу 4 , 7 , 10 , 11 , 12 , 13 . Однако, хотяЭти методы были отличными ступенями, существует ряд препятствий, которые все еще встречаются, с которыми этот протокол способен справиться. Во-первых, многие из нынешних процедур изолируют клетки от диссоциированной ткани и пытаются использовать либо основной компонентный анализ, либо иерархическую кластеризацию post-hoc для определения классификации клеток. Опираясь на эти инструменты для классификации подтипов, может не дать надежных результатов и может заставить искать новые способы проверки этих данных для корреляции генетического маркера с функциональным типом клетки. Требование диссоциации в других протоколах может иногда приводить к повреждению тканей и может приводить к отделению нейрональных процессов, что приводит к потенциальной потере мРНК. Кроме того, в диссоциированных клеточных препаратах стрессовые реакции могут начинать влиять на транскриптомы этих клеток 14 . Этот протокол преодолевает эти трудности, определяя тип функциональных клеток до изоляции, и он лучше поддерживает hЗа счет сохранения целостности ткани сетчатки. Один метод был введен в 2014 году и состоял из анализа in vivo транскриптома живых клеток 15 . Хотя этот метод позволяет исследовать транскриптом с минимальным механическим разрушением ткани, ему не хватает способности классифицировать определенные типы клеток в ткани до исследования их транскриптомов без использования очень специфической мыши-репортера. Наш протокол не требует специального репортера, так как мы используем заполнение клеток и электрофизиологию для характеристики клеток перед их изоляцией. Другим ограничением этого предыдущего протокола является то, что он требует определенной длины волны для возбуждения фотоактивируемого элемента, тогда как наш протокол позволяет использовать флуоресцентный репортер и флуоресцентный краситель, которые легко доступны или могут быть выбраны каждой лабораторией индивидуально. Тем не менее, другие лаборатории вышли замуж заOphysiology и transcriptomics для изучения клеточного разнообразия. Использование патч-зажимных записей для характеристики функции клетки до ее изоляции было выполнено на диссоциированных нейронах 16, а в некоторых случаях предшествовало использование анализа микрочипов 17 для этих исследований. Этими подходами сталкиваются те же самые осложнения, поскольку они требуют диссоциации тканей или использования технологии микрочипов, которая основана на гибридизации образцов с доступными зондами. Одним из последних достижений является разработка Patch-Seq, метода, который сочетает использование патч-зажимных записей и технологию RNA-Seq для понимания клеток из цельных мозговых срезов 18 . Хотя этот метод имеет сходство с протоколом, представленным здесь, снова важно отметить, что наш подход позволяет ткани оставаться неповрежденным для здоровья клеток. Здесь мы представляем протокол для optimizatКоторый создает высококачественные одноячеечные библиотеки для использования РНК-Seq для получения высокой глубины считывания и покрытия карт.

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	<tbody>
		<tr height="20">
			<td height="20" style="height:20px;width:257px;">Ames&#39; Medium</td>
			<td style="width:171px;">Sigma Aldrich</td>
			<td style="width:108px;">A1420-10X1L</td>
			<td style="width:372px;"></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Sodium Bicarbonate</td>
			<td>Sigma Aldrich</td>
			<td>S8875</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">K-gluconate</td>
			<td>Spectrum Chemical</td>
			<td>PO178</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">EGTA</td>
			<td>Sigma Aldrich</td>
			<td>E4378</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">HEPES</td>
			<td>Sigma Aldrich</td>
			<td>H3375</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Diethyl pyrocarbonate (DEPC)</td>
			<td>Sigma Aldrich</td>
			<td>D5758</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Alexa Fluor 594 Hydrazide</td>
			<td>Invitrogen</td>
			<td>A10442</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Collagenase</td>
			<td>Worthington Biochemical&#160;</td>
			<td>LS005273</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Hyaluronidase</td>
			<td>Worthington Biochemical&#160;</td>
			<td>LS002592</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Petri dish (35mm diameter)</td>
			<td>Thermo Fisher Scientific</td>
			<td>153066</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Ophthalmologic scissors</td>
			<td>Fine Science Tools</td>
			<td>15000-00</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">#5 Forceps</td>
			<td>Fine Science Tools</td>
			<td>11252-30</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Microplate Shaker</td>
			<td>Fisher Scientific</td>
			<td>13-687-708</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Glass Micropipette</td>
			<td>Sutter</td>
			<td>BF120-69-10</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Micropipette Puller</td>
			<td>Sutter</td>
			<td></td>
			<td>P-1000 horizontal pipette puller</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">1mL syringe</td>
			<td>Fisher Scientific</td>
			<td>14-823-2F</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Flexible tubing</td>
			<td>Fisher Scientific</td>
			<td>14-171</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">TCL lysis buffer</td>
			<td>Qiagen</td>
			<td>1031576</td>
			<td>Lysis Buffer 1</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">&#946;-mercaptoethanol</td>
			<td>Sigma Aldrich</td>
			<td>M3148</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">RNase-Free Water</td>
			<td>Qiagen</td>
			<td>129112</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">0.2 ml PCR tubes</td>
			<td>Eppendorf</td>
			<td>30124359</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Ethyl Alcohol, Pure</td>
			<td>Sigma Aldrich</td>
			<td>E7023</td>
			<td>Ethanol</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Analog Vortex Mixer</td>
			<td>Thermo Fisher Scientific</td>
			<td>02215365</td>
			<td>Vortex</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Mini Centrifuge</td>
			<td>Thermo Fisher Scientific</td>
			<td>05-090-100</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Agencourt RNAClean XP Beads</td>
			<td>Beckman Coulter</td>
			<td>A63987</td>
			<td>RNA magnetic beads</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">MagnaBlot II Magnetic Separator</td>
			<td>Promega</td>
			<td>V8351</td>
			<td>Magnetic stand</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">1.5 ml MCT Graduated Tubes</td>
			<td>Thermo Fisher Scientific</td>
			<td>05-408-129</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Smart-Seq v4 Ultra Low Input RNA Kit</td>
			<td>Clontech</td>
			<td>634888</td>
			<td>Reagents for Reverse Transcription and PCR Amplification</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">10X Lysis Buffer</td>
			<td></td>
			<td></td>
			<td>Lysis Buffer 2</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">5X Ultra Low First-Strand Buffer</td>
			<td></td>
			<td></td>
			<td>Buffer 1</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">3&#39; SMART-Seq CDS Primer II A</td>
			<td></td>
			<td></td>
			<td>Primer II</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">SMART-Seq v4 Oligonucleotide</td>
			<td></td>
			<td></td>
			<td>Oligonucleotide</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">SMARTScribe Rverse Transcriptase</td>
			<td></td>
			<td></td>
			<td>Reverse Transcriptase</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">2X SeqAmp PCR Buffer</td>
			<td></td>
			<td></td>
			<td>PCR Buffer</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">PCR Primer II A</td>
			<td></td>
			<td></td>
			<td>PCR Primer</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">SeqAmp DNA Polymerase</td>
			<td></td>
			<td></td>
			<td>DNA Polymerase</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Mastercycler pro S</td>
			<td>Eppendorf</td>
			<td>950030020</td>
			<td>Thermocycler</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Agencourt AMPure XP Beads</td>
			<td>Beckman Coulter</td>
			<td>A63881</td>
			<td>DNA magnetic beads</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">2100 Bioanalyzer</td>
			<td>Agilent Technologies</td>
			<td>G2939AA</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">HS Bioanalyzer Chips &#38; Reagents</td>
			<td>Agilent Technologies</td>
			<td>5067-4626</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Qubit HS Assay Kit</td>
			<td>Thermo Fisher Scientific</td>
			<td>Q32851</td>
			<td>For the calculation of sample concentrations</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Qubit Assay Tubes</td>
			<td>Thermo Fisher Scientific</td>
			<td>Q32856</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Qubit 2.0 Fluorometer</td>
			<td>Thermo Fisher Scientific</td>
			<td>Q32866</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Nextera XT DNA Sample Preparation Kit</td>
			<td>Illumina</td>
			<td>FC-131-1024</td>
			<td>Reagents for Tagmentation and Index Coupling</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">TD Buffer</td>
			<td></td>
			<td></td>
			<td>Buffer 2</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">ATM</td>
			<td></td>
			<td></td>
			<td>Tagmentation Mix</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">NT Buffer</td>
			<td></td>
			<td></td>
			<td>Tagmentation Neutralizing Buffer</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">NPM</td>
			<td></td>
			<td></td>
			<td>PCR Master Mix</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Nextera XT Index Kit</td>
			<td>Illumina</td>
			<td>FC-131-1001</td>
			<td>Indices for Tagmentation</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">N501</td>
			<td></td>
			<td></td>
			<td>White 1</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">N502</td>
			<td></td>
			<td></td>
			<td>White 2</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">N701</td>
			<td></td>
			<td></td>
			<td>Orange 1</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">N702</td>
			<td></td>
			<td></td>
			<td>Orange 2</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">HiSeq 2500</td>
			<td>Illumina</td>
			<td>SY-401-2501</td>
			<td>For completing sequencing of samples</td>
		</tr>
	</tbody>
</table>

single-cell rna-seq of defined subsets of retinal ganglion cells

Открытие маркеров, специфичных для типа клеток, может дать представление о клеточной функции и происхождении клеточной гетерогенности. С недавним толчком для лучшего понимания нейронного разнообразия важно идентифицировать гены, экспрессия которых определяет различные субпопуляции клеток. Сетчатка служит отличной моделью для исследования разницы в центральной нервной системе, так как она состоит из нескольких основных типов клеток. Изучение каждого крупного класса клеток дало генетические маркеры, которые облегчают идентификацию этих популяций. Однако в каждом из этих основных классов клеток сетчатки существуют многочисленные подтипы клеток, и лишь немногие из этих подтипов имеют известные генетические маркеры, хотя многие из них характеризуются морфологией или функцией. Знание генетических маркеров для индивидуальных подтипов сетчатки позволило бы изучать и отображать мозговые мишени, связанные со специфическими визуальными функциями, и также может давать представление о генных сетях, которыеПоддерживать клеточное разнообразие. Существующие способы идентификации генетических маркеров подтипов имеют недостатки, такие как классификация типов клеток после секвенирования. Это создает проблему для анализа данных и требует строгих методов проверки, чтобы гарантировать, что кластеры содержат ячейки одной и той же функции. Мы предлагаем метод идентификации морфологии и функциональности клетки до выделения и секвенирования, что позволит более легко идентифицировать маркеры, специфичные для подтипов. Этот метод может быть распространен на не-нейронные типы клеток, а также на редкие популяции клеток с незначительными вариациями. Этот протокол обеспечивает отличное качество данных, так как многие библиотеки обеспечивают глубину чтения более 20 миллионов считываний для отдельных ячеек. Эта методология преодолевает многие из препятствий, представленных одноячеечной РНК-Seq, и может быть подходящей для исследователей, стремящихся к профилированию типов клеток простым и высокоэффективным способом.

Типы клеток легко классифицируются после введения красителя На рисунке 1 показан пример GFP + RGC до и после заполнения флуоресцентными индикаторами. Эта клетка была идентифицирована на основе ее экспрессии GFP в трансгенной линии...

Watch this Scientific Journal Video about Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells at JoVE.com

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

Здесь мы представляем комбинаторный подход для классификации типов нейронных клеток до выделения и для последующей характеристики одноклеточных транскриптомов. Этот протокол оптимизирует подготовку образцов для успешного секвенирования РНК (РНК-Seq) и описывает методологию, разработанную специально для углубленного понимания клеточного разнообразия.

Одноклеточная РНК-Seq определенных подмножеств клеток сетчатки ганглия

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 overall goal of this procedure is to isolate fluorescently labeled single cells from live whole mount retinas. This method can help answer key questions in neuroscience. Such as how many subtypes of a particular neuronal class exist and what are the genetic markers for each subtype?The main advantage of this technique is that we forgo the need for retinal tissue dissociation, allowing the cells to survive in a healthier environment prior to isolation. The implications of this technique extend to any fluorescently labeled cell population and can thus be applied to other systems to understand cellular diversity and function in health and disease. Generally, individuals new to this method will struggle, because this technique relies on the ability of the researcher to patch-clamp a cell without compromising the viability of the cell.Future demonstration of this method is critical as RNA isolation steps may be difficult to learn, because the small amount of RNA may easily degrade if not handled properly and quickly. To begin this procedure, poke the cornea with a needle and cut it away at the border of the cornea and sclera. Then, remove the lens using forceps.Gently make a tear in the sclera and sever the optic nerve where the retina and sclera meet. Carefully finish removing the sclera from the retina. Next, remove the transparent vitreous.Slice the retinas in half and store them in the oxygenated extracellular solution at room temperature until use. When ready to mount the tissue in the recording chamber, transfer a piece of retina to the enzyme solution, diluted in 500 microliters of oxygenated extracellular solution in a petri dish, and incubate it for two minutes at room temperature on a shaker. Subsequently, wash the retina in the oxygenated extracellular solution and transfer it to a glass bottom recording chamber with a plastic transfer pipette.After that, use forceps to carefully flatten the tissue with the photoreceptor layer facing down. Remove excess fluid using a pipette and anchor the tissue using a platinum ring with nylon mesh. Then, fill the chamber with the oxygenated extracellular solution and mount it on to a microscope stage.Perfuse the tissue with the oxygenated extracellular solution at two to four milliliters per minute. To prepare for this procedure, pulse some glass micropipettes for electrophysiological recordings using a micropipette puller. Observe the ganglion cell layer using IR-DIC optics.Then, identify the GFP plus ganglion cells using epifluorescence at about 480 nanometers. Next, locate the pipette filled with intracellular solution in DIC. Apply slight positive pressure and zero any voltage offsets on the amplifier.Subsequently, lower the glass micropipette on a GFP positive cell and apply test voltage command steps to monitor the seal resistance. The negative pressure should form a gigaohm seal between the pipette and the cell membrane. After forming a stable seal, rupture the membrane by applying brief pulses of negative pressure to gain whole cell access.Wait one to two minutes for the dendrites of the cell to fill with fluorescent tracer. In this step, carefully extract the cell cytoplasmic content into the pipette by applying negative pressure with a ten milliliter syringe. In the meantime, monitor the extraction in DIC by visualizing the cell body decreasing in size.After extracting the cytoplasmic contents, lift the pipette carefully off from the tissue and quickly remove the pipette from the solution. Next, quickly remove the pipette from the headstage holder and rinse the pipette tip briefly with DEPC-treated H2O. Then, connect the pipette to a one milliliter syringe via the tight-fitting tubing.Immediately expel the cells into ten microliters of lysis buffer one in the 0.2 milliliter PCR tubes. Briefly centrifuge the tubes in a table-top mini centrifuge at 2000 times g for ten seconds. Following that immediately flash freeze the samples on dry ice for five minutes.After freezing, store them at negative 80 degrees Celsius for up to two weeks for best results. To prepare for this procedure, set up a magnetic separator device by taping the top part of an inverted P20 or P200 tip holder to the 96 well magnetic stand. Then, prepare fresh 70%ethanol at approximately one milliliter per sample.Remove the RNA magnetic beads from 4 degree C storage and thaw them at room temperature. Once the RNA beads are at room temperature, vortex them for 30 seconds to ensure that the solution is well mixed. After that, thaw the cells at room temperature for one minute.Then, add five microliters of Rnase-free H2O to each sample and pipette up and down. Afterward, add 22 microliters of RNA beads to each tube and mix thoroughly. Incubate the samples at room temperature for five minutes to allow the RNA to interact and bind with the magnetic beads.Following that, place the tubes on a magnetic separator device for eight minutes. Before proceeding, ensure that the supernatant is clear. Observe the beads from one palette and be sure not to detach it from the side of tube during pipetting.Remove the supernatant from the samples and add 150 microliters of 70%ethanol. Then, remove the ethanol and repeat the wash two more times. Allow the samples to air dry for six minutes.Check intermittently to see if more ethanol has been collected at the bottom of the tube and remove it accordingly. Remember it is critical to dry the beads appropriately. If the beads are not dry enough, ethanol may be carried through with the eluent and will decrease the total yields, while over dried beads can result in the loss of RNA.While the samples are drying, prepare 10x reaction buffer by combining 19 microliters of lysis buffer two and one microliter of Rnase inhibitor. Briefly spin it down and keep it on ice. Once the samples are dry and the bead pellets no longer appear glossy, remove the tubes from the magnetic separator and add 9.5 microliters of Rnase-free H2O to rehydrate the samples.Then, place the samples on ice and add one microliter of 10x reaction buffer to each sample. This image shows the ganglion cell layer of the retina, visualized using IR-DIC in the whole mount retina preparation. The same preparation was visualized in epifluorescence at about 480 nanometers to identify the GFP positive ganglion cells.This image shows a GFP positive cell that was targeted for patch-clamp recording and filled with a fluorescent tracer. Confocal image of ipRGC dendrites imaged in the on and off sublamina of the inner plexiform layer allows for the classification of these cell types This bioanalyzer output shows the examples of libraries that have undergone reverse transcription, amplification, and purification. Lanes one to three show ideal DNA smears, while lane four represents a poorly processed sample.The control lane should contain two clean peaks at the marker sizes of 35 bp and 10380 bp. Here is a detailed trace of one successfully prepared library with high-intensity around 2 kb. This trace also demonstrates a successful preparation, but with the smear centered around 500 bp.This image shows the bioanalyzer output following tagmentation, amplification and purification of the samples. The detailed trace of a successfully tagmented sample can be seen here, corresponding to the sample in lane one. Incomplete tagmentation will result in a trace such as the one seen here, warranting retagmentation with a fresh dilution.After watching this video you should have a good understanding of how to isolate RNA from the fluorescently labeled cell types in the intact retina. While attempting this procedure, it's important to remember that RNA is very sensitive to degradation and that having healthy retinal cells is the key. Once mastered, this technique can be done in two days if it is performed properly.Following this procedure, other methods like qPCR, NC2 hybridization, or immunohistochemistry, can be performed in order to answer additional questions, like whether identified genes are specific to a given cellular subtype. This technique has paved the way for researchers in the field of neuroscience, trying to understand heterogeneity of neurons in various brain regions. Understanding this heterogeneity will allow for future studies of cellular function and connectivity in molecularly identified populations.

single-cell-rna-seq-of-defined-subsets-of-retinal-ganglion-cells

Research

JoVE Journal

Neuroscience

An Isolated Retinal Preparation to Record Light Response from Genetically Labeled Retinal Ganglion Cells

The first steps in vertebrate vision take place when light stimulates the rod and cone photoreceptors of the retina 1. This information is then segregated into what are known as the ON and OFF pathways. The photoreceptors signal light information to the bipolar cells (BCs), which depolarize in response to increases (On BCs) or decreases (Off BCs) in light intensity. This segregation of light information is maintained at the level of the retinal ganglion cells (RGCs), which have dendrites stratifying in either the Off sublamina of the inner plexiform layer (IPL), where they receive direct excitatory input from Off BCs, or stratifying in the On sublamina of the IPL, where they receive direct excitatory input from On BCs. This segregation of information regarding increases or decreases in illumination (the On and Off pathways) is conserved and signaled to the brain in parallel.
The RGCs are the output cells of the retina, and are thus an important cell to study in order to understand how light information is signaled to visual nuclei in the brain. Advances in mouse genetics over recent decades have resulted in a variety of fluorescent reporter mouse lines where specific RGC populations are labeled with a fluorescent protein to allow for identification of RGC subtypes 2 3 4 and specific targeting for electrophysiological recording. Here, we present a method for recording light responses from fluorescently labeled ganglion cells in an intact, isolated retinal preparation. This isolated retinal preparation allows for recordings from RGCs where the dendritic arbor is intact and the inputs across the entire RGC dendritic arbor are preserved. This method is applicable across a variety of ganglion cell subtypes and is amenable to a wide variety of single-cell physiological techniques.

This article provides a description of how to dissect and record from the isolated retinal preparation in mouse. In particular, we describe how to record light responses from a fluorescently labeled ganglion cell population and subsequently identify and analyze its morphology.

Изолированные сетчатки Подготовка к записи Света Ответ Генетически Маркированный ганглиозных клеток сетчатки

The first steps in vertebrate vision take place when light stimulates the rod and cone photoreceptors of the retina 1.  This information is then ...

Transfection of Mouse Retinal Ganglion Cells by in vivo Electroporation

The targeting and refinement of RGC projections to the midbrain is a popular and powerful model system for studying how precise patterns of neural connectivity form during development. In mice, retinofugal projections are arranged in a topographic manner and form eye-specific layers in the Lateral Geniculate Nucleus (dLGN) of the thalamus and the Superior Colliculus (SC). The development of these precise patterns of retinofugal projections has typically been studied by labeling populations of RGCs with fluorescent dyes and tracers, such as horseradish peroxidase1-4. However, these methods are too coarse to provide insight into developmental changes in individual RGC axonal arbor morphology that are the basis of retinotopic map formation. They also do not allow for the genetic manipulation of RGCs.
Recently, electroporation has become an effective method for providing precise spatial and temporal control for delivery of charged molecules into the retina5-11. Current retinal electroporation protocols do not allow for genetic manipulation and tracing of retinofugal projections of a single or small cluster of RGCs in postnatal mice. It has been argued that postnatal in vivo electroporation is not a viable method for transfecting RGCs since the labeling efficiency is extremely low and hence requires targeting at embryonic ages when RGC progenitors are undergoing differentiation and proliferation6. 
In this video we describe an in vivo electroporation protocol for targeted delivery of genes, shRNA, and fluorescent dextrans to murine RGCs postnatally. This technique provides a cost effective, fast and relatively easy platform for efficient screening of candidate genes involved in several aspects of neural development including axon retraction, branching, lamination, regeneration and synapse formation at various stages of circuit development. In summary we describe here a valuable tool which will provide further insights into the molecular mechanisms underlying sensory map development.

Transfection of Mouse Retinal Ganglion Cells by in vivo Electroporation

We demonstrate an in vivo electroporation protocol for transfecting single or small clusters of retinal ganglion cells (RGCs) and other retinal cell types in postnatal mice over a wide range of ages. The ability to label and genetically manipulate postnatal RGCs in vivo is a powerful tool for developmental studies.

Трансфекция Мышь ганглиозных клеток сетчатки при В естественных условиях Электропорация

The targeting and refinement of RGC projections to the midbrain is a popular and powerful model system for studying how precise patterns of neural ...

An Optic Nerve Crush Injury Murine Model to Study Retinal Ganglion Cell Survival

Injury to the optic nerve can lead to axonal degeneration, followed by a gradual death of retinal ganglion cells (RGCs), which results in irreversible vision loss. Examples of such diseases in human include traumatic optic neuropathy and optic nerve degeneration in glaucoma. It is characterized by typical changes in the optic nerve head, progressive optic nerve degeneration, and loss of retinal ganglion cells, if uncontrolled, leading to vision loss and blindness.
The optic nerve crush (ONC) injury mouse model is an important experimental disease model for traumatic optic neuropathy, glaucoma, etc. In this model, the crush injury to the optic nerve leads to gradual retinal ganglion cells apoptosis. This disease model can be used to study the general processes and mechanisms of neuronal death and survival, which is essential for the development of therapeutic measures. In addition, pharmacological and molecular approaches can be used in this model to identify and test potential therapeutic reagents to treat different types of optic neuropathy.
Here, we provide a step by step demonstration of (I) Baseline retrograde labeling of retinal ganglion cells (RGCs) at day 1, (II) Optic nerve crush injury at day 4, (III) Harvest the retinae and analyze RGC survival at day 11, and (IV) Representative result.

This protocol shows how to retrogradely label retinal ganglion cells, and how to subsequently make an optic nerve crush injury in order to analyze retinal ganglion cell survival and apoptosis. It is an experimental disease model for different types of optic neuropathy, including glaucoma.

Зрительный нерв размозжение мышиной моделью для изучения сетчатки выживания клеток ганглия

Injury to the optic nerve can lead to axonal degeneration, followed by a gradual death of retinal ganglion cells (RGCs), which results in irreversible ...

Single-cell Profiling of Developing and Mature Retinal Neurons

Highly specialized, but exceedingly small populations of cells play important roles in many tissues. The identification of cell-type specific markers and gene expression programs for extremely rare cell subsets has been a challenge using standard whole-tissue approaches. Gene expression profiling of individual cells allows for unprecedented access to cell types that comprise only a small percentage of the total tissue1-7. In addition, this technique can be used to examine the gene expression programs that are transiently expressed in small numbers of cells during dynamic developmental transitions8.
This issue of cellular diversity arises repeatedly in the central nervous system (CNS) where neuronal connections can occur between quite diverse cells9. The exact number of distinct cell types is not precisely known, but it has been estimated that there may be as many as 1000 different types in the cortex itself10. The function(s) of complex neural circuits may rely on some of the rare neuronal types and the genes they express. By identifying new markers and helping to molecularly classify different neurons, the single-cell approach is particularly useful in the analysis of cell types in the nervous system. It may also help to elucidate mechanisms of neural development by identifying differentially expressed genes and gene pathways during early stages of neuronal progenitor development.
As a simple, easily accessed tissue with considerable neuronal diversity, the vertebrate retina is an excellent model system for studying the processes of cellular development, neuronal differentiation and neuronal diversification. However, as in other parts of the CNS, this cellular diversity can present a problem for determining the genetic pathways that drive retinal progenitors to adopt a specific cell fate, especially given that rod photoreceptors make up the majority of the total retinal cell population11. Here we report a method for the identification of the transcripts expressed in single retinal cells (Figure 1). The single-cell profiling technique allows for the assessment of the amount of heterogeneity present within different cellular populations of the retina2,4,5,12. In addition, this method has revealed a host of new candidate genes that may play role(s) in the cell fate decision-making processes that occur in subsets of retinal progenitor cells8. With some simple adjustments to the protocol, this technique can be utilized for many different tissues and cell types.

A method for the isolation of single retinal cells and subsequent amplification of their cDNAs is described. Single-cell transcriptomics reveals the degree of cellular heterogeneity present in a tissue and uncovers new marker genes for rare cell populations. The accompanying protocol can be adjusted to suit many different cell types.

Одноклеточный профилирования развивающихся и зрелых нейронов сетчатки

Highly specialized, but exceedingly small populations of cells play important roles in many tissues. The identification of cell-type specific markers and ...

Viral Tracing of Genetically Defined Neural Circuitry

Classical methods for studying neuronal circuits are fairly low throughput. Transsynaptic viruses, particularly the pseudorabies (PRV) and rabies virus (RABV), and more recently vesicular stomatitis virus (VSV), for studying circuitry, is becoming increasingly popular. These higher throughput methods use viruses that transmit between neurons in either the anterograde or retrograde direction.
Recently, a modified RABV for monosynaptic retrograde tracing was developed. (Figure 1A). In this method, the glycoprotein (G) gene is deleted from the viral genome, and resupplied only in targeted neurons. Infection specificity is achieved by substituting a chimeric G, composed of the extracellular domain of the ASLV-A glycoprotein and the cytoplasmic domain of the RABV-G (A/RG), for the normal RABV-G1. This chimeric G specifically infects cells expressing the TVA receptor1. The gene encoding TVA can been delivered by various methods2-8. Following RABV-G infection of a TVA-expressing neuron, the RABV can transmit to other, synaptically connected neurons in a retrograde direction by nature of its own G which was co-delivered with the TVA receptor. This technique labels a relatively large number of inputs (5-10%)2 onto a defined cell type, providing a sampling of all of the inputs onto a defined starter cell type.
We recently modified this technique to use VSV as a transsynaptic tracer9. VSV has several advantages, including the rapidity of gene expression. Here we detail a new viral tracing system using VSV useful for probing microcircuitry with increased resolution. While the original published strategies by Wickersham et al.4 and Beier et al.9 permit labeling of any neurons that project onto initially-infected TVA-expressing-cells, here VSV was engineered to transmit only to TVA-expressing cells (Figure 1B). The virus is first pseudotyped with RABV-G to permit infection of neurons downstream of TVA-expressing neurons. After infecting this first population of cells, the virus released can only infect TVA-expressing cells. Because the transsynaptic viral spread is limited to TVA-expressing cells, presence of absence of connectivity from defined cell types can be explored with high resolution. An experimental flow chart of these experiments is shown in Figure 2. Here we show a model circuit, that of direction-selectivity in the mouse retina. We examine the connectivity of starburst amacrine cells (SACs) to retinal ganglion cells (RGCs).

A method of tracing synaptically connected neurons is described. We use TVA specificity of an upstream cell to probe whether a cell population of interest receives synaptic input from genetically defined cell types.

Вирусный отслеживание генетически определенных нервной системы

Classical methods for studying neuronal circuits are fairly low throughput. Transsynaptic viruses, particularly the pseudorabies (PRV) and rabies virus ...

Implementing Dynamic Clamp with Synaptic and Artificial Conductances in Mouse Retinal Ganglion Cells

Ganglion cells are the output neurons of the retina and their activity reflects the integration of multiple synaptic inputs arising from specific neural circuits. Patch clamp techniques, in voltage clamp and current clamp configurations, are commonly used to study the physiological properties of neurons and to characterize their synaptic inputs. Although the application of these techniques is highly informative, they pose various limitations. For example, it is difficult to quantify how the precise interactions of excitatory and inhibitory inputs determine response output. To address this issue, we used a modified current clamp technique, dynamic clamp, also called conductance clamp 1, 2, 3 and examined the impact of excitatory and inhibitory synaptic inputs on neuronal excitability. This technique requires the injection of current into the cell and is dependent on the real-time feedback of its membrane potential at that time. The injected current is calculated from predetermined excitatory and inhibitory synaptic conductances, their reversal potentials and the cell's instantaneous membrane potential. Details on the experimental procedures, patch clamping cells to achieve a whole-cell configuration and employment of the dynamic clamp technique are illustrated in this video article. Here, we show the responses of mouse retinal ganglion cells to various conductance waveforms obtained from physiological experiments in control conditions or in the presence of drugs. Furthermore, we show the use of artificial excitatory and inhibitory conductances generated using alpha functions to investigate the responses of the cells.

This video article illustrates the set-up, the procedures to patch cell bodies and how to implement dynamic clamp recordings from ganglion cells in whole-mount mouse retinae. This technique allows the investigation of the precise contribution of excitatory and inhibitory synaptic inputs, and their relative magnitude and timing to neuronal spiking.

Реализация динамического Хомут с Synaptic и искусственного проводимости в мыши ганглиозных клеток сетчатки

Ganglion cells are the output neurons of the  retina and their activity reflects the integration of multiple synaptic inputs  arising from specific neural ...

Retrograde Labeling of Retinal Ganglion Cells in Adult Zebrafish with Fluorescent Dyes

As retrograde labeling retinal ganglion cells (RGCs) can isolate RGCs somata from dying sites, it has become the gold standard for counting RGCs in RGCs survival and regeneration experiments. Many studies have been performed in mammalian animals to research RGCs survival after optic nerve injury. However, retrograde labeling of RGCs in adult zebrafish has not yet been reported, though some alternative methods can count cell numbers in retinal ganglion cell layers (RGCL). Considering the small size of the adult zebrafish skull and the high risk of death after drilling on the skull, we open the skull with the help of acid-etching and seal the hole with a light curing bond, which could significantly improve the survival rate. After absorbing the dyes for 5 days, almost all the RGCs are labeled. As this method does not need to transect the optic nerve, it is irreplaceable in the research of RGCs survival after optic nerve crush in adult zebrafish. Here, we introduce this method step by step and provide representative results.

We introduce an efficient method to retrograde label retinal ganglion cells (RGCs) in adult zebrafish.

Ретроградная Маркировка ганглиозных клеток сетчатки в взрослых данио рерио флуоресцентными красителями

As retrograde labeling retinal ganglion cells (RGCs) can isolate RGCs somata from dying sites, it has become the gold standard for counting RGCs in RGCs ...

RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord

In ovo electroporation of the chick neural tube is a fast and inexpensive method for identification of gene function during neural development. Genome wide analysis of differentially expressed transcripts after such an experimental manipulation has the potential to uncover an almost complete picture of the downstream effects caused by the transfected construct. This work describes a simple method for comparing transcriptomes from samples of transfected embryonic spinal cords comprising all steps between electroporation and identification of differentially expressed transcripts. The first stage consists of guidelines for electroporation and instructions for dissection of transfected spinal cord halves from HH23 embryos in ribonuclease-free environment and extraction of high-quality RNA samples suitable for transcriptome sequencing. The next stage is that of bioinformatic analysis with general guidelines for filtering and comparison of RNA-Seq datasets in the Galaxy public server, which eliminates the need of a local computational structure for small to medium scale experiments. The representative results show that the dissection methods generate high quality RNA samples and that the transcriptomes obtained from two control samples are essentially the same, an important requirement for detection of differential expression genes in experimental samples. Furthermore, one example is provided where experimental overexpression of a DNA construct can be visually verified after comparison with control samples. The application of this method may be a powerful tool to facilitate new discoveries on the function of neural factors involved in spinal cord early development.

This video shows the basic steps for performing whole transcriptome analysis on dissected chick embryonic spinal cord samples after transfection with in ovo electroporation.

Секвенирование РНК анализ дифференциальных экспрессии генов в электропорации Чик эмбрионального спинного мозга

In ovo electroporation of the chick neural tube is a fast and inexpensive method for identification of gene function during neural development. Genome ...

Optical Coherence Tomography: Imaging Mouse Retinal Ganglion Cells In Vivo

Structural changes in the retina are common manifestations of ophthalmic diseases. Optical coherence tomography (OCT) enables their identification in vivo&#8212;rapidly, repetitively, and at a high resolution. This protocol describes OCT imaging in the mouse retina as a powerful tool to study optic neuropathies (OPN). The OCT system is an interferometry-based, non-invasive alternative to common post mortem histological assays. It provides a fast and accurate assessment of retinal thickness, allowing the possibility to track changes, such as retinal thinning or thickening. We present the imaging process and analysis with the example of the Opa1delTTAG mouse line. Three types of scans are proposed, with two quantification methods: standard and homemade calipers. The latter is best for use on the peripapillary retina during radial scans; being more precise, is preferable for analyzing thinner structures. All approaches described here are designed for retinal ganglion cells (RGC) but are easily adaptable to other cell populations. In conclusion, OCT is efficient in mouse model phenotyping and has the potential to be used for the reliable evaluation of therapeutic interventions.

Optical Coherence Tomography: Imaging Mouse Retinal Ganglion Cells In Vivo

This manuscript describes a protocol for the in vivo imaging of the mouse retina with high-resolution spectral domain optical coherence tomography (SD-OCT). It focuses on retinal ganglion cells (RGC) in the peripapillary region, with several scanning and quantifying approaches described.

Оптическая когерентная томография: Визуализация мыши сетчатки ганглия клетки в естественных условиях

Structural changes in the retina are common manifestations of ophthalmic diseases. Optical coherence tomography (OCT) enables their identification in ...

Partial Optic Nerve Transection in Rats: A Model Established with a New Operative Approach to Assess Secondary Degeneration of Retinal Ganglion Cells

Previous studies have shown that the secondary degeneration of retinal ganglion cells (RGCs) occurs commonly in glaucoma. Partial optic nerve transection is considered a useful and reproducible model. Compared with other optic nerve injury models used commonly for assessing secondary degeneration, e.g. complete optic nerve transection and optic nerve crush models, the partial optic nerve transection model is superior as it distinguishes primary from secondary degeneration in situ. Therefore, it serves as an excellent tool for evaluating secondary degeneration. This study describes a novel operative approach of partial optic nerve transection by directly accessing the area of the retrobulbar optic nerve through the orbital lateral wall of the eyeball. Moreover, we present a newly designed, low cost surgical instrument to assist with transection. As demonstrated by the representative results in distinguishing the boundary of primary and secondary injury areas, the new approach and instrument ensures high efficiency and stability of the model by providing adequate space for surgical operation. This in turn makes it easy to separate the meningeal sheath and ophthalmic vessels from the optic nerve before transection. An additional benefit is that this space-saving operative approach improves the investigators&#39; ability to administer drugs, carriers, or selective RGC tracers to the stump of the partially transected optic nerve, allowing the exploration of mechanisms behind secondary injury in RGCs, in a new way.

Secondary degeneration of retinal ganglion cells (RGCs) occurs commonly in glaucoma. This study describes an innovative operative approach for partial optic nerve transection. The use of this space-saving operative approach extends the model's application range, and allows exploration of secondary injury mechanisms in RGCs in a new way.

Перерезка частичное зрительного нерва у крыс: модель с новой постановляющей части подход к оценке вторичной дегенерации сетчатки ганглия клеток

Previous studies have shown that the secondary degeneration of retinal ganglion cells (RGCs) occurs commonly in glaucoma. Partial optic nerve transection ...