Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San Diego, United States
- Department of Cellular & Molecular Medicine, University of California, San Diego, United States
- Sanford Consortium for Regenerative Medicine, United States
- Biomedical Graduate Studies Program, University of California, San Diego, United States
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, United States
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, United States
- Ludwig Institute for Cancer Research, United States
Figures
Figure 1 with 1 supplement
T2D-associated risk variants are enriched in stretch enhancers of pancreatic progenitors independent of islet stretch enhancers.
(A) Schematic illustrating the stepwise differentiation of human embryonic stem cells (hES) into pancreatic progenitors (solid arrows) and lineage relationship to islets (dotted arrow). …
Figure 1—figure supplement 1
Characterization of typical and stretch enhancers in pancreatic developmental intermediates and islets.
(A) Diagram illustrating incorporation of histone modification and CTCF ChIP-seq data to generate chromatin state calls via ChromHMM. (B) Percentage of the genome covered by defined chromatin states …
Figure 2 with 1 supplement
Candidate target genes of pancreatic progenitor-specific stretch enhancers regulate developmental processes.
(A) Schematic illustrating identification of pancreatic progenitor-specific stretch enhancers (PSSE). (B) Heatmap showing density of H3K27ac ChIP-seq and ATAC-seq reads at PSSE, centered on …
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Figure 2—source data 1
Chromosomal coordinates of pancreatic progenitor-specific stretch enhancers (PSSE).
- https://cdn.elifesciences.org/articles/59067/elife-59067-fig2-data1-v1.xlsx
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Figure 2—source data 2
Enriched gene ontology terms for PSSE-associated genes.
- https://cdn.elifesciences.org/articles/59067/elife-59067-fig2-data2-v1.xlsx
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Figure 2—source data 3
Proportion of variants nominally associated with beta cell functional traits.
- https://cdn.elifesciences.org/articles/59067/elife-59067-fig2-data3-v1.xlsx
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Figure 2—source data 4
Tissue identity of downloaded data from ROADMAP consortium.
- https://cdn.elifesciences.org/articles/59067/elife-59067-fig2-data4-v1.xlsx
Figure 2—figure supplement 1
Characterization of pancreatic progenitor-specific stretch enhancers.
(A) Percentage of PSSE overlapping with at least one ATAC-seq peak at PP2. Enrichment analysis comparing observed and expected overlap based on random genomic regions of the same size and located on …
Figure 3 with 1 supplement
Identification of T2D risk variants associated with pancreatic progenitor-specific stretch enhancers.
(A) Manhattan plot showing T2D association p-values (from Mahajan et al., 2018) for 10,738 variants mapping within PSSE. The dotted line shows the threshold for Bonferroni correction (p=4.66 × 10−6).…
Figure 3—figure supplement 1
Activity of T2D risk-associated pancreatic progenitor-specific stretch enhancers across human tissues.
(A) mRNA levels (measured in fragments per kilobase per million fragments mapped [FPKM]) at PP2 and in human embryonic pancreas (54 and 58 days gestation, Emb Pan) of all genes expressed (FPKM ≥1) …
Figure 4 with 2 supplements
A T2D risk-associated LAMA1 pancreatic progenitor-specific stretch enhancer regulates LAMA1 expression specifically in pancreatic progenitors.
(A) (Top) Locus plots showing T2D association p-values for variants in a 35 kb window (hg19 chr18:7,050,000–7,085,000) at the LAMA1 locus and LAMA1 PSSE (red box). Fine mapped variants within the …
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Figure 4—source data 1
Genes downregulated in ∆LAMA1Enh PP2 stage cells compared to control cells (p adj. <0.05).
- https://cdn.elifesciences.org/articles/59067/elife-59067-fig4-data1-v1.xlsx
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Figure 4—source data 2
Genes upregulated in ∆LAMA1Enh PP2 stage cells compared to control cells (p adj. <0.05).
- https://cdn.elifesciences.org/articles/59067/elife-59067-fig4-data2-v1.xlsx
Figure 4—figure supplement 1
Deletion of the LAMA1-associated pancreatic progenitor-specific enhancer does not affect pancreatic lineage specification.
(A) Odds ratio estimates (points) and 95% CIs (lines) for rs10502347 association with T2D and metabolic GWAS traits. Significant associations are colored black, non-significant are colored light …
Figure 4—figure supplement 2
Deletion of LAMA1 does not affect pancreatic lineage specification.
(A) Schematic illustrating CRISPR-Cas9-mediated deletion strategy of LAMA1 to generate ∆LAMA1 hESC clonal line. (B) Immunofluorescent staining for Laminin in control and ∆LAMA1 PP2 cells …
Figure 5 with 3 supplements
A T2D risk-associated CRB2 pancreatic progenitor-specific stretch enhancer regulates CRB2 expression specifically in pancreatic progenitors.
(A) (Top) Locus plots showing T2D association p-values for variants in a 35 kb window (hg19 chr9:126,112,000–126,147,000) at the CRB2 locus and CRB2 PSSE (red box). Fine mapped variants within the …
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Figure 5—source data 1
Genes downregulated in ∆CRB2Enh PP2 stage cells compared to control cells (p adj. <0.05).
- https://cdn.elifesciences.org/articles/59067/elife-59067-fig5-data1-v1.xlsx
Figure 5—figure supplement 1
Activity of CRB2- and PGM1-associated pancreatic progenitor-specific stretch enhancers across human tissues.
(A) (Top) Locus plots showing T2D association p-values for variants in a 43 kb window (hg19 chr1:64,084,000–64,127,000) at the PGM1 locus and PGM1 PSSE (red box). Fine mapped variants within the 99% …
Figure 5—figure supplement 2
Deletion of the CRB2-associated pancreatic progenitor-specific enhancer does not affect pancreatic lineage specification.
(A) Schematic illustrating CRISPR-Cas9-mediated deletion strategy of CRB2-associated PSSE to generate independent ∆CRB2Enh hESC clones with different DNA cleavage products. (B) Flow cytometry …
Figure 5—figure supplement 3
Deletion of CRB2 does not affect pancreatic lineage specification.
(A) Schematic illustrating CRISPR-Cas9-mediated deletion strategy of CRB2 to generate ∆CRB2 hESC clonal line. (B) Immunofluorescent staining for CRB2 in control and ∆CRB2 PP2 cells (representative …
Figure 6 with 4 supplements
lama1 and crb2 regulate pancreas morphogenesis and beta cell differentiation.
(A,B) Representative 3D renderings of Tg(ptf1a:eGFP)jh1 control zebrafish embryos (A,A’) and lama1 morphants (B,B’) stained with DAPI (nuclei, blue) and antibody against insulin (red); n ≥ 15 …
Figure 6—figure supplement 1
Laminin and Crb are expressed in zebrafish pancreas progenitors.
(A,B) Confocal images of 36 hr post fertilization (hpf) Tg(ptf1a:eGFP)jh1 zebrafish foregut endoderm labeled with DAPI (nuclei, grey) and antibodies against Nkx6.1 (blue; pancreatic progenitors) and …
Figure 6—figure supplement 2
Validation of morpholinos targeting lama1.
Confocal images (3D rendered) of 32–34 hpf Tg(ptf1a:eGFP)jh1 zebrafish foregut endoderm labeled with DAPI (nuclei, grey) and anti-Laminin antibodies (red). (A–A’’) Z-focal plane image of pancreatic …
Figure 6—figure supplement 3
Validation of morpholinos targeting crb2a and crb2b.
(A,B) 3D renderings of 32–34 hpf Tg(ptf1a:eGFP)jh1 zebrafish foregut endoderm labeled with DAPI (nuclei, grey) and anti-Crb2a antibodies (red). (A–A’’) Z-focal plane image showing Crb2a labeled …
Figure 6—figure supplement 4
crb2b but not crb2a regulates pancreatic beta cell differentiation.
Quantification of beta (insulin+) cell nuclei per embryo in Tg(ptf1a:eGFP)jh1 control zebrafish embryos and crb2a or crb2b morphants at 78 hr post fertilization (hpf). p adj. = 0.91 and 4.4 × 10−2 …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | APC Mouse monoclonal IgG1, κ Isotype Control | BD Pharmingen | Cat# 555751, RRID:AB_398613 | Flow cytometry (1:100) |
| Antibody | Chicken polyclonal anti-GFP | Aves Labs | Cat# GFP-1020, RRID:AB_10000240 | Immunohistochemistry (1:200) |
| Antibody | Cy3-conjugated donkey polyclonal anti-mouse | Jackson ImmunoResearch Labs | Cat# 715-165-150, RRID:AB_2340813 | Immunofluorescence (1:1000) |
| Antibody | DyLight 488-conjugated donkey polyconal anti-goat | Jackson ImmunoResearch Labs | Cat# 705-545-003, RRID:AB_2340428 | Immunofluorescence (1:500) |
| Antibody | Goat polyclonal anti-CTCF | Santa Cruz Biotechnology | Cat# SC-15914X, RRID:AB_2086899 | ChIP-seq (4 ug) |
| Antibody | Goat polyclonal anti-FOXA1 | Abcam | Cat# ab5089, RRID:AB_304744 | ChIP-seq (4 ug) |
| Antibody | Goat polyclonal anti-FOXA2 | Santa Cruz Biotechnology | Cat# sc-6554, RRID:AB_2262810 | ChIP-seq (4 ug) |
| Antibody | Goat polyclonal anti-GATA4 | Santa Cruz Biotechnology | Cat# sc-1237, RRID:AB_2108747 | ChIP-seq (4 ug) |
| Antibody | Goat polyclonal anti-PDX1 | Abcam | Cat# ab47383, RRID:AB_2162359 | Immunofluorescence (1:500) |
| Antibody | Guinea pig polyclonal anti-Insulin | Biomeda | Cat# v2024 | Immunohistochemistry (1:200) |
| Antibody | Mouse monoclonal anti-Crb2a | ZIRC | Cat# Zs-4 | Immunohistochemistry (1:100) |
| Antibody | Mouse polyclonal anti-GATA6 | Santa Cruz Biotechnology | Cat# sc-9055, RRID:AB_2108768 | ChIP-seq (4 ug) |
| Antibody | Mouse monoclonal anti-NKX6.1 | Developmental Studies Hybridoma Bank | Cat# F64A6B4, RRID:AB_532380 | Immunofluorescence (1:300) |
| Antibody | Mouse monoclonal anti-NKX6.1-Alexa Fluor 647 | BD Biosciences | Cat# 563338, RRID:AB_2738144 | Flow cytometry (1:5) |
| Antibody | Mouse monoclonal anti-NKX6.1 | Developmental Studies Hybridoma Bank | Cat# F55A10, RRID:AB_532378 | Immunohistochemistry (1:10) |
| Antibody | Mouse monoclonal anti-PDX1-PE | BD Biosciences | Cat# 562161, RRID:AB_10893589 | Flow cytometry (1:10) |
| Antibody | PE Mouse monoclonal IgG1, κ Isotype Control | BD Pharmingen | Cat# 555749, RRID:AB_396091 | Flow cytometry (1:100) |
| Antibody | Rabbit polyclonal anti-CRB2 | Sigma | Cat # SAB1301340 | Immunofluorescence (1:500) |
| Antibody | Rabbit polyclonal anti-H3K27ac | Active Motif | Cat# 39133, RRID:AB_2561016 | ChIP-seq (4 ug) |
| Antibody | Rabbit polyclonal anti-H3K4me1 | Abcam | Cat# ab8895, RRID:AB_306847 | ChIP-seq (4 ug) |
| Antibody | Rabbit polyclonal anti-HNF6 | Santa Cruz Biotechnology | Cat# sc-13050, RRID:AB_2251852 | ChIP-seq (4 ug) |
| Antibody | Rabbit polyclonal anti-laminin | Sigma | Cat# L9393, RRID:AB_477163 | Immunohistochemistry (1:100) Immunofluorescence (1:30) |
| Antibody | Rabbit monoclonal anti-panCrb | Jensen Laboratory, University of Massachusetts, Amherst | N/A | Immunohistochemistry (1:100) |
| Antibody | Rabbit polyclonal anti-PDX1 | Beta Cell Biology Consortium | AB1068 | ChIP-seq (4 ug) |
| Antibody | Rabbit polyclonal anti-SOX9 | Chemicon | Cat# 5535, RRID:AB_2239761 | ChIP-seq (4 ug) |
| Cell line (Homo-sapiens) | CyT49 | ViaCyte, Inc | NIHhESC-10–0041, RRID:CVCL_B850 | Male |
| Cell line (Homo-sapiens) | H1 | WiCell Research Institute | NIHhESC-10–0043, RRID:CVCL_9771 | Male |
| Chemical compound, drug | 2-Mercaptoethanol | Thermo Fisher Scientific | Cat# 21985023 | |
| Chemical compound, drug | Accutase | Thermo Fisher Scientific | Cat# 00-4555-56 | |
| Chemical compound, drug | B-27 supplement | Thermo Fisher Scientific | Cat# 17504044 | |
| Chemical compound, drug | Bovine Albumin Fraction V | Life Technologies | Cat# 15260037 | |
| Chemical compound, drug | D-(+)-Glucose Solution, 45% | Sigma-Aldrich | Cat# G8769 | |
| Chemical compound, drug | DAPI | Invitrogen | Cat# D1306 | Immunohistochemistry (1:200) |
| Chemical compound, drug | DMEM High Glucose | VWR | Cat# 16750–082 | |
| Chemical compound, drug | DMEM/F12 [-] L-glutamine | VWR | Cat# 15–090-CV | |
| Chemical compound, drug | DMEM/F12 with L-Glutamine, HEPES | Corning | Cat# 45000–350 | |
| Chemical compound, drug | DMF | EMD Millipore | Cat# DX1730 | |
| Chemical compound, drug | DPBS | Thermo Fisher Scientific | Cat# 21–031-CV | |
| Chemical compound, drug | DTT | Sigma | Cat# D9779 | |
| Chemical compound, drug | Fetal Bovine Serum | Thermo Fisher Scientific | Cat# MT35011CV | |
| Chemical compound, drug | Glutamax | Thermo Fisher Scientific | Cat# 35050–079 | |
| Chemical compound, drug | GlutaMAX | Thermo Fisher Scientific | Cat# 35050061 | |
| Chemical compound, drug | Hoechst 33342 | Thermo Fisher Scientific | Cat# H3570 | |
| Chemical compound, drug | HyClone Dulbecco’s Modified Eagles Medium | Thermo Fisher Scientific | Cat# SH30081.FS | |
| Chemical compound, drug | IGEPAL-CA630 | Sigma | Cat# I8896 | |
| Chemical compound, drug | Illumina tagmentation enzyme | Illumina | Cat# FC-121–1030 | |
| Chemical compound, drug | Insulin-Transferrin-Selenium (ITS) | Thermo Fisher Scientific | Cat# 41400045 | |
| Chemical compound, drug | Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) | Thermo Fisher Scientific | Cat# 51500–056 | |
| Chemical compound, drug | KAAD-Cyclopamine | Toronto Research Chemicals | Cat# K171000 | |
| Chemical compound, drug | K-acetate | Sigma | Cat# P5708 | |
| Chemical compound, drug | KnockOut SR XenoFree | Thermo Fisher Scientific | Cat# A1099202 | |
| Chemical compound, drug | LDN-193189 | Stemgent | Cat# 04–0074 | |
| Chemical compound, drug | Matrigel | Corning | Cat# 356231 | |
| Chemical compound, drug | MCDB 131 | Thermo Fisher Scientific | Cat# 10372–019 | |
| Chemical compound, drug | Mg-acetate | Sigma | Cat# M2545 | |
| Chemical compound, drug | mTeSR1 Complete Kit - GMP | STEMCELL Technologies | Cat# 85850 | |
| Chemical compound, drug | NEBNext High-Fidelity 2X PCR Master Mix | NEB | Cat# M0541 | |
| Chemical compound, drug | Non-Essential Amino Acids | Thermo Fisher Scientific | Cat# 11140050 | |
| Chemical compound, drug | O.C.T. Compound | Sakura Finetek USA | Cat# 25608–930 | |
| Chemical compound, drug | Penicillin-Streptomycin | Thermo Fisher Scientific | Cat# 15140122 | |
| Chemical compound, drug | Polyethylenimine (PEI) | Polysciences | Cat# 23966–1 | |
| Chemical compound, drug | Protease inhibitor | Roche | Cat# 05056489001 | |
| Chemical compound, drug | Retinoic acid | Sigma-Aldrich | Cat# R2625 | |
| Chemical compound, drug | RNA ScreenTape Sample Buffer | Agilent Technologies | Cat# 5067–5577 | |
| Chemical compound, drug | ROCK Inhibitor Y-27632 | STEMCELL Technologies | Cat# 72305 | |
| Chemical compound, drug | RPMI 1640 [-] L-glutamine | VWR | Cat# 15–040-CV | |
| Chemical compound, drug | SANT-1 | Sigma-Aldrich | Cat# S4572 | |
| Chemical compound, drug | Sodium Bicarbonate | Sigma-Aldrich | Cat# NC0564699 | |
| Chemical compound, drug | Tamoxifen | Sigma | Cat# T5648 | |
| Chemical compound, drug | TGF-β RI Kinase Inhibitor IV | Calbiochem | Cat# 616454 | |
| Chemical compound, drug | TPB | Calbiochem | Cat# 565740 | |
| Chemical compound, drug | Tranylcypromine | Cayman Chemical | Cat# 10010494 | |
| Chemical compound, drug | Tris-acetate | Thermo Fisher Scientific | Cat# BP-152 | |
| Chemical compound, drug | TTNPB | Enzo Life Sciences | Cat# BML-GR105 | |
| Chemical compound, drug | Vectashield Antifade Mounting Medium | Vector Laboratories | Cat# H-1000 | |
| Chemical compound, drug | XtremeGene 9 | Roche | Cat# 6365787001 | |
| Commercial assay | High Sensitivity D1000 ScreenTape | Agilent Technologies | Cat# 5067–5584 | |
| Commercial assay, kit | RNA ScreenTape | Agilent Technologies | Cat# 5067–5576 | |
| Commercial assay, kit | RNA ScreenTape Ladder | Agilent Technologies | Cat# 5067–5578 | |
| Commercial assay, kit | BD Cytofix/Cytoperm Plus Fixation/Permeabilization Solution Kit | BD Biosciences | Cat# 554715 | |
| Commercial assay, kit | ChIP-IT High Sensitivity Kit | Active Motif | Cat# 53040 | |
| Commercial assay, kit | iQ SYBR Green Supermix | Bio-Rad | Cat# 1708884 | |
| Commercial assay, kit | iScript cDNA Synthesis Kit | Bio-Rad | Cat# 1708891 | |
| Commercial assay, kit | KAPA Library Preparation Kit (Illumina) | Kapa Biosystems | Cat# KK8234 | |
| Commercial assay, kit | KAPA Stranded mRNA-Seq Kits | Kapa Biosystems | Cat# KK8401 | |
| Commercial assay, kit | MinElute PCR purification kit | QIAGEN | Cat# 28004 | |
| Commercial assay, kit | Qubit ssDNA assay kit | Thermo Fisher Scientific | Cat# Q10212 | |
| Commercial assay, kit | RNeasy Micro Kit | QIAGEN | Cat# 74004 | |
| Genetic reagent (D. rerio) | Tg(ptf1a:eGFP)jh1 | PMID:16258076 | N/A | |
| Other | SPRIselect bead | Beckman Coulter | Cat# B23317 | |
| Recombinant protein | Activin A | R and D Systems | Cat# 338-AC/CF | |
| Recombinant protein | Human AB Serum | Valley Biomedical | Cat# HP1022 | |
| Recombinant protein | Recombinant EGF | R and D Systems | Cat# 236-EG | |
| Recombinant protein | Recombinant Heregulinβ−1 | Peprotech | Cat# 100–03 | |
| Recombinant protein | Recombinant KGF/FGF7 | R and D Systems | Cat# 251 KG | |
| Recombinant protein | Recombinant Mouse Wnt3A | R and D Systems | Cat# 1324-WN/CF | |
| Recombinant protein | Recombinant Noggin | R and D Systems | Cat# 3344 NG | |
| Sequence-based reagent | Px333 Plasmid | http://www.addgene.org/64073/ | RRID:Addgene_64073 | |
| Sequence-based reagent | LAMA1 Forward | This paper | qPCR primers | GTG ATG GCA ACA GCG CAA A |
| Sequence-based reagent | LAMA1 Reverse | This paper | qPCR primers | GAC CCA GTG ATA TTC TCT CCC A |
| Sequence-based reagent | CRB2 Forward | This paper | qPCR primers | ACC ACT GTG CTT GTC CTG AG |
| Sequence-based reagent | CRB2 Reverse | This paper | qPCR primers | TCC AGG GTC GCT AGA TGG AG |
| Sequence-based reagent | TBP Forward | This paper | qPCR primers | TGT GCA CAG GAG CCA AGA GT |
| Sequence-based reagent | TBP Reverse | This paper | qPCR primers | ATT TTC TTG CTG CCA GTC TGG |
| Sequence-based reagent | LAMA1Enh Upstream Guide | This paper | CRISPR sgRNA | GTC AAA TTG CTA TAA CAC GG |
| Sequence-based reagent | LAMA1Enh Downstream Guide | This paper | CRISPR sgRNA | CCA CTT TAA GTA TCT CAG CA |
| Sequence-based reagent | CRB2Enh Upstream Guide | This paper | CRISPR sgRNA | ATA CAA AGC ACG TGA GA |
| Sequence-based reagent | CRB2Enh Downstream Guide | This paper | CRISPR sgRNA | GAA TGC GGA TGA CGC CTG AG |
| Sequence-based reagent | lama1-ATG | PMID:16321372 | Morpholino | TCA TCC TCA TCT CCA TCA TCG CTC A Obtained from GeneTools, LLC |
| Sequence-based reagent | crb2a-SP | PMID:16713951 | Morpholino | ACG TTG CCA GTA CCT GTG TAT CCT G Obtained from GeneTools, LLC |
| Sequence-based reagent | crb2b-SP | PMID:16713951 | Morpholino | TAA AGA TGT CCT ACC CAG CTT GAA C Obtained from GeneTools, LLC |
| Sequence-based reagent | standard control MO | N/A | Morpholino | CCT CTT ACC TCA GTT ACA ATT TAT A Obtained from GeneTools, LLC |
| Software, algorithm | Adobe Illustrator v 5.1 | http://www.adobe.com/products/illustrator.html | RRID:SCR_014198 | |
| Software, algorithm | Adobe Photoshop v 5.1 | http://www.adobe.com/products/photoshop.html | RRID:SCR_014199 | |
| Software, algorithm | BEDtools v 2.26.0 | https://github.com/arq5x/bedtools2 | RRID:SCR_006646 | |
| Software, algorithm | Bioconductor | https://www.bioconductor.org/ | RRID: SCR_006442 | |
| Software, algorithm | Burrows-Wheeler Aligner v 0.7.13 | http://bio-bwa.sourceforge.net/ | RRID:SCR_010910 | |
| Software, algorithm | CENTIPEDE v 1.2 | http://centipede.uchicago.edu/ | N/A | |
| Software, algorithm | Cufflinks v 2.2.1 | http://cole-trapnell-lab.github.io/cufflinks/ | RRID:SCR_014597 | |
| Software, algorithm | deepTools2 v 3.1.3 | https://deeptools.readthedocs.io/en/develop/content/installation.html | N/A | |
| Software, algorithm | DESeq2 v 3.10 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | RRID:SCR_015687 | |
| Software, algorithm | FlowJo v10 software | https://www.flowjo.com/solutions/flowjo | RRID: SCR_008520 | |
| Software, algorithm | GraphPad Prism v 8.1.2 | https://www.graphpad.com/scientific-software/prism/ | RRID: SCR_002798 | |
| Software, algorithm | HOMER v 4.10.4 | http://homer.ucsd.edu/homer/ | RRID: SCR_010881 | |
| Software, algorithm | Juicebox Tools v 1.4 | https://github.com/aidenlab/Juicebox/wiki/Juicebox-Assembly-Tools | N/A | |
| Software, algorithm | MACS2 v 2.1.4 | http://liulab.dfci.harvard.edu/MACS/ | RRID:SCR_013291 | |
| Software, algorithm | MEME suite v 5.1.1 | http://meme-suite.org/ | RRID:SCR_001783 | |
| Software, algorithm | Metascape | http://metscape.ncibi.org | RRID:SCR_014687 | |
| Software, algorithm | Picard Tools v 1.131 | http://broadinstitute.github.io/picard/ | RRID:SCR_006525 | |
| Software, algorithm | R Project for Statistical Computing v 3.6.1 | http://www.r-project.org/ | RRID:SCR_001905 | |
| Software, algorithm | SAMtools v 1.5 | http://samtools.sourceforge.net | RRID:SCR_002105 | |
| Software, algorithm | STAR v 2.4 | https://github.com/alexdobin/STAR | N/A | |
| Software, algorithm | UCSC Genome Browser | http://genome.ucsc.edu/ | RRID:SCR_005780 | |
| Software, algorithm | vcf2diploid v 0.2.6a | https://github.com/abyzovlab/vcf2diploid | N/A | |
| Software, algorithm | ZEISS ZEN Digital Imaging for Light Microscopy | http://www.zeiss.com/microscopy/en_us/products/microscope-software/zen.html#introduction | RRID:SCR_013672 |
