JoVE Logo

Sign In

A subscription to JoVE is required to view this content. Sign in or start your free trial.

In This Article

  • Summary
  • Abstract
  • Introduction
  • Protocol
  • Results
  • Discussion
  • Disclosures
  • Acknowledgements
  • Materials
  • References
  • Reprints and Permissions

Summary

We describe a method for the isolation of endocrine cells from embryonic, neonatal and postnatal pancreases followed by single-cell RNA sequencing. This method allows analyses of pancreatic endocrine lineage development, cell heterogeneity and transcriptomic dynamics.

Abstract

Pancreatic endocrine cells, which are clustered in islets, regulate blood glucose stability and energy metabolism. The distinct cell types in islets, including insulin-secreting β cells, are differentiated from common endocrine progenitors during the embryonic stage. Immature endocrine cells expand via cell proliferation and mature during a long postnatal developmental period. However, the mechanisms underlying these processes are not clearly defined. Single-cell RNA-sequencing is a promising approach for the characterization of distinct cell populations and tracing cell lineage differentiation pathways. Here, we describe a method for the single-cell RNA-sequencing of isolated pancreatic β cells from embryonic, neonatal and postnatal pancreases.

Introduction

The pancreas is a vital metabolic organ in mammals. The pancreas is comprised of endocrine and exocrine compartments. Pancreatic endocrine cells, including insulin-producing β cells and glucagon-producing α cells, cluster together in the islets of Langerhans and coordinately regulate systemic glucose homeostasis. Dysfunction of the endocrine cells results in diabetes mellitus, which has become a major public health issue worldwide.

Pancreatic endocrine cells are derived from Ngn3+ progenitors during embryogenesis1. Later, during the perinatal period, the endocrine cells proliferate to form immature islets. These immature cells continue to develop and gradually become mature islets, which become richly vascularized to regulate blood glucose homeostasis in adults2.

Although a group of transcriptional factors has been identified that regulate β cell differentiation, the precise maturation pathway of β cells is still unclear. Moreover, the β cell maturation process also involves the regulation of cell number expansion3,4 and the generation of cellular heterogeneity5,6. However, the regulatory mechanisms of these processes have not been well studied.

Single-cell RNA-sequencing is a powerful approach that can profile cell subpopulations and trace cell lineage developmental pathways7. Taking advantage of this technology, the key events that occur during pancreatic islet development can be deciphered at the single-cell level8. Among the single-cell RNA-sequencing protocols, Smart-seq2 allows the generation of full-length cDNA with improved sensitivity and accuracy, and the use of standard reagents at lower cost9. Smart-seq2 takes approximately two days to construct a cDNA library for sequencing10.

Here, we propose a method for the isolation of fluorescence-labeled β cells from the pancreases of fetal to adult Ins1-RFP transgenic mice11, using fluorescence-activated cell sorting (FACS), and the performance of transcriptomic analyses at the single-cell level, using Smart-seq2 technology (Figure 1).This protocol can be extended to analyze the transcriptomes of all pancreatic endocrine cell types in normal, pathological and aging states.

Protocol

All methods described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of Peking University.

1. Pancreas Isolation

  1. For E17.5 (embryonic day 17.5) embryos:
    1. Estimate embryonic day 0.5 based on the time point when the vaginal plug appears.
    2. Sacrifice the pregnant mice by CO2 administration. Spray the abdominal fur with 70% alcohol.
    3. Make a V-shaped incision with scissors from the genital area extending to the ribs. This process will completely open the abdominal cavity.
    4. Dissect the uterus out of the abdominal cavity and place it in a 10 cm dish containing cold PBS.
    5. Dissect the embryos from the uterus with thin-tipped forceps under a stereomicroscope, removing other tissues, such as the placenta and umbilical cord. Place all embryos in a 10 cm dish containing cold PBS.
    6. Tear open the embryos’ abdominal cavity and dig out the visceral tissue with elbow tweezers. Transfer the visceral tissue into a 6 cm black-bottom dish containing cold PBS.
    7. The pancreas is located in the upper left part of the abdomen and attaches to the stomach, spleen and duodenum (yellow dotted line in Figure 2A)12. Detach the pancreases from the visceral tissue using forceps and pool the pancreatic tissue together into a 20 mL vial containing 5 mL of 0.5 mg/mL cold collagenase solution: 0.5 mg/mL collagenase P in isolation buffer (HBSS containing 10 mM HEPES, 1 mM MgCl2, 5 mM Glucose, pH 7.4).
  2. For P0-P15 (postnatal day 0-15) mice:
    1. Sacrifice and fix the mouse by adhering the limbs to a piece of benchtop protector with tape. Spray the abdominal fur with 70% alcohol.
    2. Completely open the abdominal cavity as described in step 1.1.3. Pull the bowel out and to the left side of the mouse. This procedure will expose the duodenal, gastric, and splenic lobes of the pancreas. Carefully dissect all lobes of the pancreas (Figure 2B)12 and pool the pancreatic tissue together into a 20 mL vial containing 5 mL of 0.5 mg/mL cold collagenase solution.
  3. For P18-P60 (postnatal day 18-60) mice:
    1. Prepare the collagenase solution. Keep on ice until ready for use.
    2. Sacrifice the mouse and open the abdominal cavity as mentioned above (step 1.1.2 and 1.1.3).
      NOTE: Do not hurt the liver, any wound to the liver will reduce the flow pressure into the bile duct and reduce the perfusion efficiency of the following step.
    3. Remove the xiphoid. Pull the bowel out and to the right side of the mouse, and push the left and right medial lobes of the liver to each side to expose the gallbladder (white arrow in Figure 2C) and the common bile duct.
    4. Clamp the duodenum with a pair of small vessel clamps at the upper and lower position, flanking the site where the bile duct enters the duodenum (Figure 2D).
      NOTE: Do not clamp the gastric or splenic lobes of the pancreas. The collagenase solution will not flow into the gastric and splenic lobe of the pancreas in the next step if clamped.
    5. Fill a syringe with 5 mL of 0.5 mg/mL cold collagenase solution and insert a 30 G needle into the gallbladder. Carefully and smoothly, manipulate the needle through the common bile duct.
    6. Perfuse the pancreas by injecting 1–5 mL of 0.5 mg/mL cold collagenase solution, depending on the size of the mouse. The injection should be slow and constant to prevent the needle from slipping out of the duct and to prevent the intestine from bursting under high liquid pressure. The injection is complete when the pancreas is fully expanded.
    7. Dissect the pancreas (The yellow dotted line in Figure 2D) out of the abdominal cavity using forceps immediately after perfusion. Place the tissue in a 20 mL vial containing 5 mL of 0.5 mg/mL cold collagenase solution. If manipulating more than one mouse at a time, perfuse the mice one by one and pool the tissues into cold collagenase solution in a 20 mL vial until all mice have been dissected.

2. Collagenase Digestion and Islet Isolation

  1. Place the 20 mL vial containing the pancreatic tissue into a 37 °C water bath and incubate for 3 min to equilibrate the temperature.
  2. Gently shake the tube for another 3 to 5 min. If the pancreatic tissue is fully inflated, it will gradually dissociate into small tissue pieces until it is finally dispersed uniformly. The digestion time varies depending on the pancreas size and the perfusion efficiency.
  3. Filter the digested product through a 0.25 mm nylon strainer into a new 50 mL centrifuge tube. Throughly wash the strainer using a 20 mL syringe containing ice-cold PBS.
  4. For E17.5-P15 pancreases, skip to step 3.1.
  5. For P18-P60 pancreases, centrifuge at 200 x g for 1 min and discard the supernatant. Re-suspend the tissue with cold PBS.
  6. Pour 5 mL of the tissue suspension into a 6 cm black-bottom dish. The pancreatic islets are small, compact, milky white structures and acinar tissue is loose and translucent white. Pick islets with a 200 μL pipette and transfer them into a 1.5 mL tube containing a small amount of cold PBS.

3. Trypsin Digestion of Pancreatic Tissue or Islets

  1. Centrifuge the tube containing pancreatic tissue or islets at 200 x g for 1 min at 4 °C and discard the supernatant without disturbing the pellet.
  2. Re-suspend the pellet with 0.25% trypsin-EDTA and incubate in a 37 °C water bath. After 4 min of incubation, gently and occasionally aspirate (pipette) for 1 min using 200 μL tips.
    NOTE: For E17.5-P3 pancreases, add 1 mL trypsin-EDTA. For P4-P15 pancreases, add 3 mL trypsin-EDTA. For 100-300 islets, add 1 mL trypsin-EDTA. Adjust the volume of trypsin-EDTA according to the amount of tissue.
  3. Stop the digestion by adding 0.4x volume of cold fetal bovine serum (FBS) and mix by gentle vortex.
  4. Centrifuge at 250 x g for 3 min at 4 °C. Discard the supernatant without disturbing the pellet.
  5. Re-suspend the cells with 200 μL cold FACS buffer (HBSS containing 1% FBS, pH 7.4). Transfer cells to a 5 mL FACS tube.
  6. Quickly spin the FACS tube to allow the cell suspension to pass through the filter to remove undigested large tissue debris. The single cell suspension in the tube is now ready for FACS sorting.

4. Single-cell Lysis

  1. Prepare cell lysis buffer.
    NOTE: Perform all experiments under a UV-sterilized hood with laminar flow. All tubes, plates and pipette tips should be RNase-/DNase-free. Decontaminate the hood and pipettes with RNase away solution before use.
    1. Thaw the reagents on ice: dNTP (10 mM), oligo-dT primer (10 μM), and ERCC stock solution (1:20).
    2. Dilute the ERCC to 1:5 x 105 with nuclease-free water.
    3. Calculate the volume of cell lysis buffer needed. Add 0.1 μL of RNase inhibitor (40 U/μL), 1.9 μL of 0.2% (vol/vol) Triton X-100, 1 μL of dNTP, 1 μL of oligo-dT primer, and 0.05 μL of diluted ERCC to a final volume of 4.05 μL for each cell.
    4. Aliquot the cell lysis buffer into 0.2 mL thin-wall 8-stripe PCR tubes or 96-well plates. Centrifuge the tubes or plates for 30 s at 4 °C.
      Note: Centrifuge 0.2 mL thin-wall 8-stripe PCR tubes at 7500 x g and 96-well plates at 800 x g in the following steps.
  2. Single-cell picking and lysis.
    1. Manually pick FACS sorted Ins1-RFP+ single cells in FACS buffer into 8-strip PCR tubes using a 30–40 µm capillary pipette, or directly sort Ins1-RFP+ single cells into 96-well plates. The volume containing a single cell is considered to be less than 0.3 μL.
      Note: Use forward scatter height (FSC-H) vs forward scatter area (FSC-A) gating strategy for doublet discrimination, FSC-H vs side scatter area (SSC-A) for debris and fluorescence gating for Ins1-RFP+ cell (Figure 3A-3C) sorting. For the picking method, sort the target cells into a 1.5 mL tube containing 300 μL FACS buffer. The appropriate final concentration is 5–10 cells/μL. Adjust the buffer volume accordingly. For the plate collection method, sort a single-cell into each well of a 96-well plate following the manual of instrument.7,13
    2. Vortex the tubes or plates to lyse the cells and release the RNA. Centrifuge the tubes or plates for 30 s at 4 °C and immediately place them on ice.
      Note: The cells can be stored at -80 °C for one week.

5. Single-cell cDNA Amplification

  1. Reverse transcription (RT).
    1. Thaw the RT reagents (Table 1) on ice.
    2. Incubate the samples at 72 °C for 3 min and immediately put the tubes or plates on ice for at least 1 min. Briefly centrifuge the tubes or plates for 30 s at 4 °C.
      Note: Use a thermal cycler with a 105 °C heated lid for all incubations.
    3. Prepare the RT mix for all reactions, as described in Table 1.
    4. Dispense 5.7 μL of RT mix to each sample to bring the volume to a total of 10 μL. Gently vortex the mix and centrifuge for 30 s at 4 °C.
    5. Place the samples into a thermal cycler and start the RT program as follows: 42 °C for 90 min, 10 cycles (50 °C for 2 min, 42 °C for 2 min), 70 °C for 15 min and hold at 4 °C.
  2. PCR pre-amplification.
    1. Thaw the PCR reagents (Table 2) on ice.
    2. Prepare the PCR mix for all reactions, as described in Table 2.
    3. Dispense 15 μL of PCR mix to each sample, which contains the first-strand reactions. Gently vortex the mix and centrifuge for 30 s at 4 °C.
    4. Place the samples into a thermal cycler and start the following PCR program: 98 °C for 3 min, 18 cycles (98 °C for 20 s, 67 °C for 15 s, 72 °C for 6 min), 72 °C for 5 min and hold at 4 °C.
      NOTE: The PCR product can be stored at 4 °C for less than one week or at -20 °C / -80 °C for up to 6 months.
  3. PCR purification.
    1. Add 25 μL of re-suspended DNA purification beads (1x) to each sample from the previous step and mix well by vortex. Then, quickly spin the tube or plates at room temperature to collect the liquid but avoid the settlement of beads.
      NOTE: Equilibrate DNA purification beads to room temperature for 15 min and vortex thoroughly before use.
    2. Incubate for 5 min at room temperature.
    3. Place the tube or plate on an appropriate magnetic stand until the solution is clear, then carefully remove and discard the supernatant.
    4. Add 200 μL of freshly prepared 80% ethanol to wash the beads while in the magnetic stand, incubate for 30 s, then carefully remove and discard the ethanol solution.
      NOTE: The 80% (vol/vol) ethanol solution should be freshly prepared each time.
    5. Repeat step 5.3.4 for a total of two washes.
    6. Carefully remove and discard the remaining ethanol solution and air dry the beads while the tube or plate is on the magnetic stand.
      NOTE: Avoid over-drying the beads to ensure the maximum elution efficiency.
    7. Add 11 μL of nuclease-free water to elute the DNA target from the beads and mix well by vortex. Then, quickly spin the tube or plate and place it on a magnetic stand until the solution is clear. Transfer 10 μL of the sample to a new PCR tube.
      Note: If dimers exist after a single round of purification, based on cDNA size distribution detection, purify again to remove the dimers completely. The dimers can influence the cDNA yield calculation if allowed to remain in the sample.
  4. Quality check of cDNA.
    1. Randomly choose samples to detect the cDNA total yield using a fluorometer.
    2. Evaluate the marker gene expression levels by real-time PCR (qPCR) (Figure 4E). Remove 1 μL of the sample to dilute 40 times and perform qPCR using a 384-well plate. Prepare the qPCR mix as described in Table 3. Cycling conditions: 95 °C for 10 min, 45 cycles (95 °C for 10 s, 60 °C for 15 s, 72 °C for 15 s).
    3. Randomly choose samples to detect the size distribution using a parallel capillary electrophoresis instrument.

6. cDNA Library Construction

  1. Tagmentation reaction by the Tn5 transposase.
    1. Detect the cDNA total yield of qPCR-selected cells from step 5.4.2 using a fluorometer. Use 2 ng of cDNA as the starting material.
    2. Thaw the tagmentation reaction reagents (Table 4) on ice.
    3. Prepare the tagmentation reaction in a 0.2 mL thin-wall 8-stripe PCR tube, as described in Table 4, and mix carefully by vortex. Then, quickly spin down the solution at room temperature.
    4. Incubate the samples at 55 °C for 10 min and hold at 4 °C.
    5. Immediately add 2 μL of 5x TS to each sample containing the tagmented DNA to stop the reaction. Mix carefully by vortex, and then quickly spin down the solution at room temperature.
    6. Incubate the mixture for 5 min at room temperature. The DNA should be processed for the final enrichment PCR immediately.
  2. Amplification of adapter-ligated fragments.
    1. Thaw the PCR reagents (Table 5) on ice.
    2. Prepare the enrichment PCR mix, as described in Table 5, and mix carefully by vortex. Then, quickly spin down the solution at room temperature.
    3. Perform the PCR by using the following program: 72 °C for 10 min, 98 °C for 30 s, 8 cycles (98 °C for 15 s, 60 °C for 30 s, 72 °C for 3 min), 72 °C for 5 min and hold at 4 °C.
      NOTE: The number of cycles depends on the expected library DNA amount.
  3. PCR purification with size selection.
    1. Add 14 μL of re-suspended DNA purification beads (0.7 x) to each sample from the previous step and mix well by vortex. Then, quickly spin the tube at room temperature to collect the liquid but avoid the settlement of beads.
      NOTE: Equilibrate DNA purification beads to room temperature for 15 min and vortex thoroughly before use.
    2. Incubate for 5 min at room temperature.
    3. Place the tube on an appropriate magnetic stand until the solution is clear, carefully transfer the supernatant to a new tube strip and discard the previous tube stripe.
    4. Add 3 μL of re-suspended DNA purification beads (0.15x) to each sample in the tube stripe and mix well by vortex. Then, quickly spin the tube at room temperature.
    5. Incubate for 5 min at room temperature.
    6. Place the tube or plate on an appropriate magnetic stand until the solution is clear, then carefully remove and discard the supernatant.
    7. Add 200 μL of freshly prepared 80% ethanol to wash the beads while in the magnetic stand, incubate for 30 s, then carefully remove and discard the ethanol solution.
      NOTE: The 80% (vol/vol) ethanol solution should be freshly prepared each time.
    8. Repeat step 6.3.7 for a total of two washes.
    9. Carefully remove and discard the remaining ethanol solution and air dry the beads while the tube or plate is on the magnetic stand.
      NOTE: Avoid over-drying the beads to ensure the maximum elution efficiency.
    10. Add 11 μL of nuclease-free water to elute the DNA target from the beads and mix well by vortex. Then, quickly spin the tube or plate and place it on a magnetic stand until the solution is clear. Transfer 10 μL of the sample to a new tube stripe.
  4. Quality check of final cDNA library.
    1. Measure the concentration of each library using a fluorometer and check the size distribution using a parallel capillary electrophoresis instrument.
      Note: The DNA yield is typically between 15–25 ng for each library. The fragments ranging from 250 bp to 450 bp will be observed. If dimers remain after purification, as confirmed by the size distribution check, purify with 1 x DNA purification beads one more time.
  5. Library pooling
    1. Based on the approximate fragment size, pool equal amounts of DNA from each sample, ensuring that none of them contain the same combinations of N6XX and N8XX adapters.

7. DNA Sequencing

  1. Subject barcoded libraries to 51 bp single-end sequencing using a high-throughput sequencing system. Perform the sequencing following the manufacturer's protocol. The sequencing depth of each cell is about 1 million reads on average8, at least 0.5 million reads per cell14.

8. Bioinformatics Analyses

  1. Sequencing quality evaluation and alignment.
    1. Evaluate the quality of sequenced reads using FastQC (v0.11.3)15 with the following parameters: “fastqc --extract -o output_dir input_fastq”.
    2. Merge the mouse genome with the ERCC sequences using the command “cat mm10.fa ERCC.fa >mm10_ERCC.fa”.
    3. Build bowtie2 (v2.2.5)16 index with the following parameters: “bowtie2-build mm10_ERCC.fa mm10_ERCC”.
    4. Align reads using tophat2 (v2.1.0)17 with the following parameters: “tophat2 -o output_dir -G gene.gtf --transcriptome-index trans_index mm10_ERCC input_fastq”.
  2. Quantify gene expression levels.
    1. Count mapped reads for each gene using HTSeq (v 0.6.0)18 with the following parameters: ‘‘htseq-count -f bam -r pos -s no -a 30 accepted_hits.bam gene.gtf > read_count.txt’’.
    2. Normalize the gene expression levels to transcripts per million (TPM)19.
  3. Quality control of cells.
    1. Exclude cells with fewer than 0.5 million mapped reads or fewer than 4,000 genes (TPM > 1).
      NOTE: the criterion of exclusion depends on the cell types and sequence depth.
    2. Retain cells expressing endocrine markers (e.g., Ins1 for β cells, Gcg for α cells), and exclude cells expressing non-endocrine markers (e.g., Spi1 for leukocytes).
  4. Principal component analysis (PCA)
    1. Identify highly variable genes according to ERCC spike-ins, as previously described20.
    2. Perform PCA using the function “PCA” in the R package FactoMineR (v1.31.4)21, with log2(TPM + 0.1) of highly variable genes.
    3. Visualize the PCA results with ggplot2 (v2.0.0)22.
  5. Hierarchical clustering.
    1. Identify genes with the highest principal component (PC) loadings using the “dimdesc” function FactoMineR (v1.31.4)21.
    2. Perform hierarchical clustering using the function “heatmap.2“ in the R package gplots (v3.0.1)23, with log2 (TPM + 1) relative values of high PC loading genes.

Results

Pancreases were dissected from embryonic, neonatal and postnatal mice (Figure 2A and 2B). For mice older than postnatal day 18, the digestive effect depends on the degree of perfusion; therefore, the injection is the most important step for islet isolation (Figure 2C-2E and Table 6). As much collagenase was injected as was possible to fill the pancreas during thi...

Discussion

In this protocol, we demonstrated an effective and easy-to-use method for studying the single-cell expression profiles of pancreatic β cells. This method could be used to isolate endocrine cells from embryonic, neonatal and postnatal pancreases and to perform single-cell transcriptomic analyses.

The most critical step is the isolation of single β cells in good condition. Fully perfused pancreases respond better to subsequent digestion. Insufficient perfusion, which usually occurs in ...

Disclosures

The authors have nothing to disclose.

Acknowledgements

We thank the National Center for Protein Sciences, Beijing (Peking University) and the Peking-Tsinghua Center for the Life Science Computing Platform. This work was supported by the Ministry of Science and Technology of China (2015CB942800), the National Natural Science Foundation of China (31521004, 31471358, and 31522036), and funding from Peking-Tsinghua Center for Life Sciences to C.-R.X.

Materials

NameCompanyCatalog NumberComments
Collagenase PRoche11213873001
Trypsin-EDTA (0.25 %), phenol redThermo Fisher Scientific25200114
Fetal bovine serum (FBS)HycloneSH30071.03
Dumont #4 ForcepsRobozRS-4904
Dumont #5 ForcepsRobozRS-5058
30 G BD Needle 1/2" LengthBD305106
Stereo MicroscopeZeissStemi DV4
Stereo Fluorescence microscopeZeissStereo Lumar V12
CentrifugeEppendorf5810R
CentrifugeEppendorf5424R
Polystyrene Round-Bottom Tube with Cell-Strainer CapBD-Falcon352235
96-Well PCR MicroplateAxygenPCR-96-C
Silicone Sealing MatAxygenAM-96-PCR-RD
Thin Well PCR TubeExtrageneP-02X8-CF
Cell sorterBD BiosciencesBD FACSAria
Capillary pipetteSutterB100-58-10
RNaseZapAmbionAM9780
ERCC RNA Spike-In MixLife Technologies4456740
Distilled waterGibco10977
Triton X-100Sigma-AldrichT9284
dNTP mixNew England BiolabsN0447
Recombinant RNase InhibitorTakara2313
Superscript II reverse transcriptaseInvitrogen18064-014
First-strand buffer (5x)Invitrogen18064-014
DTTInvitrogen18064-014
BetaineSigma-Aldrich107-43-7
MgCl2Sigma-Aldrich7786-30-3
Nuclease-free waterInvitrogenAM9932
KAPA HiFi HotStart ReadyMix (2x)KAPA BiosystemsKK2601
VAHTS DNA Clean Beads XP beadsVazymeN411-03
Qubit dsDNA HS Assay KitInvitrogenQ32854
AceQ qPCR SYBR Green Master MixVazymeQ121-02
TruePrep DNA Library Prep Kit V2 for IlluminaVazymeTD502Include 5x TTBL, 5x TTE, 5x TS, 5x TAB, TAE
TruePrep Index Kit V3 for IlluminaVazymeTD203Include 16 N6XX and 24 N8XX
High Sensitivity NGS Fragment Analysis KitAdvanced Analytical TechnologiesDNF-474
1x HBSS without Ca2+ and Mg2+138 mM NaCl; 5.34 mM KCl
4.17 mM NaHCO3; 0.34 mM Na2HPO4
0.44 mM KH2PO4
Isolation buffer1 × HBSS containing 10 mM HEPES, 1 mM MgCl2, 5 mM Glucose, pH 7.4
FACS buffer1 × HBSS containing 15 mM HEPES, 5.6 mM Glucose, 1% FBS, pH 7.4
NaClSigma-AldrichS5886
KClSigma-AldrichP9541
NaHCO3Sigma-AldrichS6297
Na2HPO4Sigma-AldrichS5136
KH2PO4Sigma-AldrichP5655
D-(+)-GlucoseSigma-AldrichG5767
HEPESSigma-AldrichH4034
MgCl2Sigma-AldrichM2393
Oligo-dT30VN primer5'-AAGCAGTGGTATCAA
CGCAGAGTACT30VN-3'
TSO5'-AAGCAGTGGTATCAAC
GCAGAGTACATrGrG+G-3'
ISPCR primers5'-AAGCAGTGGTAT
CAACGCAGAGT-3'
Gapdh Forward primer5'-ATGGTGAAGGTC
GGTGTGAAC-3'
Gapdh Reverse primer5'-GCCTTGACT
GTGCCGTTGAAT-3'
Ins2 Forward primer5'-TGGCTTCTTC
TACACACCCA-3'
Ins2 Reverse primer5'-TCTAGTTGCA
GTAGTTCTCCA-3'

References

  1. Gu, G., Dubauskaite, J., Melton, D. A. Direct evidence for the pancreatic lineage: NGN3+ cells are islet progenitors and are distinct from duct progenitors. Development. 129 (10), 2447-2457 (2002).
  2. Oliver-Krasinski, J. M., Stoffers, D. A. On the origin of the beta cell. Genes & Development. 22 (15), 1998-2021 (1998).
  3. Dor, Y., Brown, J., Martinez, O. I., Melton, D. A. Adult pancreatic beta-cells are formed by self-duplication rather than stem-cell differentiation. Nature. 429 (6987), 41-46 (2004).
  4. Smukler, S. R., et al. The adult mouse and human pancreas contain rare multipotent stem cells that express insulin. Cell Stem Cell. 8 (3), 281-293 (2011).
  5. Dorrell, C., et al. Human islets contain four distinct subtypes of beta cells. Nature Communications. 7, 11756 (2016).
  6. Bader, E., et al. Identification of proliferative and mature beta-cells in the islets of Langerhans. Nature. 535 (7612), 430-434 (2016).
  7. Saliba, A. E., Westermann, A. J., Gorski, S. A., Vogel, J. Single-cell RNA-seq: Advances and future challenges. Nucleic Acids Research. 42 (14), 8845-8860 (2014).
  8. Qiu, W. L., et al. Deciphering pancreatic islet beta cell and alpha cell maturation pathways and characteristic features at the single-cell level. Cell Metabolism. 25 (5), 1194-1205 (2017).
  9. Picelli, S., et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nature Methods. 10 (11), 1096-1098 (2013).
  10. Picelli, S., et al. Full-length RNA-seq from single cells using Smart-seq2. Nature Protocols. 9 (1), 171-181 (2014).
  11. Piccand, J., et al. Pak3 promotes cell cycle exit and differentiation of beta-cells in the embryonic pancreas and is necessary to maintain glucose homeostasis in adult mice. Diabetes. 63 (1), 203-215 (2014).
  12. Veite-Schmahl, M. J., Regan, D. P., Rivers, A. C., Nowatzke, J. F., Kennedy, M. A. Dissection of the mouse pancreas for histological analysis and metabolic profiling. Journal of Visualized Experiments. (126), (2017).
  13. Hu, P., Zhang, W., Xin, H., Deng, G. Single cell isolation and analysis. Frontiers in Cell and Developmental Biology. 4, 116 (2016).
  14. Haque, A., Engel, J., Teichmann, S. A., Lonnberg, T. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Medicine. 9 (1), 75 (2017).
  15. . FastQC: A quality control tool for high throughput sequence data Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010)
  16. Langmead, B., Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods. 9 (4), 357-359 (2012).
  17. Kim, D., et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. 14 (4), (2013).
  18. Anders, S., Pyl, P. T., Huber, W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 31 (2), 166-169 (2015).
  19. Wagner, G. P., Kin, K., Lynch, V. J. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory in Biosciences. 131 (4), 281-285 (2012).
  20. Brennecke, P., et al. Accounting for technical noise in single-cell RNA-seq experiments. Nature Methods. 10 (11), 1093-1095 (2013).
  21. Le, S., Josse, J., Husson, F. FactoMineR: An R package for multivariate analysis. Journal of Statistical Software. 25 (1), (2008).
  22. Hadley, W. . ggplot2: Elegant graphics for data analysis. , (2009).
  23. . gplots: Various R Programming Tools for Plotting Data Available from: https://cran.r-project.org/package=gplots (2016)
  24. Marcheva, B., et al. Disruption of the clock components CLOCK and BMAL1 leads to hypoinsulinaemia and diabetes. Nature. 466 (7306), 627-631 (2010).
  25. Li, L., et al. Single-cell RNA-seq analysis maps development of human germline cells and gonadal niche interactions. Cell Stem Cell. , (2017).
  26. Qi, M., et al. Human pancreatic islet isolation: Part I: Digestion and collection of pancreatic tissue. Journal of Visualized Experiments. (27), (2009).
  27. Qi, M., et al. Human pancreatic islet isolation: Part II: Purification and culture of human islets. Journal of Visualized Experiments. (27), (2009).
  28. Teo, A. K. K., et al. Single-cell analyses of human islet cells reveal de-differentiation signatures. Cell Death Discovery. 4 (14), (2018).

Reprints and Permissions

Request permission to reuse the text or figures of this JoVE article

Request Permission

Explore More Articles

Single cell TranscriptomicsPancreatic Endocrine CellsLineage DifferentiationMaturationRegenerationDiabetesPancreatic Endocrine DiseasesCollagenase PerfusionBile DuctMouse Pancreas

This article has been published

Video Coming Soon

JoVE Logo

Privacy

Terms of Use

Policies

Research

Education

ABOUT JoVE

Copyright © 2025 MyJoVE Corporation. All rights reserved