| Antibodies |
|
|
| ARRESTIN |
Novus |
Cat# NBP!-37003 RRID: AB_2060085 |
| ATOH7 |
Novus |
Cat# NBP1-88639; RRID: AB_11034390 |
| BRN3 |
Santa Cruz |
Cat# sc-6026; RRID: AB_673441 |
| CALB1 |
Millipore |
Cat# ab1778; RRID: AB_2068336 |
| CALRET |
S.W.Ant |
Cat# 7699/4; RRID: AB_2313763 |
| ChAT |
Millipore |
Cat# AB144P; RRID: AB_2079751 |
| FABP7 |
Millipore |
Cat# ABS184; RRID: AB_10917079 |
| GFP |
Abcam |
Cat# ab13970; RRID: AB_300798 |
| Go alpha |
Millipore |
Cat# MAB3073; RRID: AB_94671 |
| HUC/D |
Invitrogen |
Cat# A-21271; RRID: AB_221448 |
| ML Opsin |
Millipore/Chemicon |
Cat# AB5407; RRID: AB_177457 |
| NR2E3 |
Perseus Proteomics |
Cat# PP-H7223-00; RRID: AB_1964331 |
| ONECUT2 |
R&D Systems |
Cat# AF6294; RRID: AB_10640365 |
| OTX2 |
R&D Systems |
Cat# BAF1979; RRID: AB_2157171 |
| OTX2 |
abcam |
Cat# AB21990; RRID: AB_776930 |
| PAX6 |
DSHB (Developmental Systems Hybridoma Bank) |
Cat# pax6; RRID:AB_528427 |
| PRDM13 |
DSHB (Developmental Systems Hybridoma Bank) |
Cat# PCRP-PRDM13-2C12; RRID:AB_2618988 |
| PRDM13 |
Rabbit |
Gift from Dr. Jane Johnson |
| RCVRN |
Chemicon |
Cat# AB5585; RRID: AB_2253622 |
| RLBP1/CRALBP |
Abcam |
Cat# Ab15051; RRID: AB_2269474 |
| SNCG |
Abnova |
Cat# H00006623M01A; RRID: AB_1581209 |
| SW Opsin |
Santa Cruz |
Cat# Sc-14363; RRID: AB_2158332 |
| SOX2 |
Santa Cruz |
Cat# SC-17320; RRID: AB_2286684 |
| SOX2 |
Abcam |
Cat# Ab15830; RRID: Ab15830 |
| TFAP2 alpha |
DSHB (Developmental Systems Hybridoma Bank) |
Cat# 5E4; RRID: AB_2056333 |
| VGLUT1 |
Synaptic Systems |
Cat# 135 304; RRID: AB_887878 |
| VSX2 |
Santa Cruz |
Cat# Sc-21690; RRID: AB_2216006 |
| Donkey anti-mouse 488 |
Jackson Immuno |
Cat# 715-546-151; RRID: AB_23440850 |
| Donkey anti-mouse 568 |
Life Technologies |
Cat# A10037;RRID: AB_2534013 |
| Donkey anti-mouse 647 |
Jackson Immuno |
Cat# 715-605-150; RRID: AB_2340862 |
| Donkey anti-goat 488 |
Life Tecnologies |
Cat# A11055; RRID: AB_142672 |
| Donkey anti-goat 568 |
Life Technologies |
Cat# A11057; RRID: AB_142581 |
| Donkey anti-goat 647 |
Jackson Immuno |
Cat# 705-605-147; RRID: AB_2340437 |
| Donkey anti-rabbit 488 |
Life Technologies |
Cat# A21206; RRID: AB_141708 |
| Donkey anti-rabbit 568 |
Life Technologies |
Cat# A100042; RRID: AB_2534017 |
| Donkey anti-rabbit 647 |
Thermo Fisher Scientific |
Cat# A-31573; RRID: AB_2536183 |
| Donkey anti-sheep 568 |
Life Technologies |
Cat# A21099; RRID: AB_141474 |
| Donkey anti-sheep 488 |
Invitrogen |
Cat# A11015; RRID: AB_141362 |
| Donkey anti-sheep 647 |
Invitrogen |
Cat# A21448; RRID: AB_10374882 |
| Donkey anti-guniea pig 488 |
Jackson Immuno |
Cat# 706-546-148; RRID: AB_2340473 |
| Donkey anti-guniea pig 594 |
Jackson Immuno |
Cat# 706-586-148; RRID: AB_2340475 |
| Donkey anti-guniea pig 647 |
Jackson Immuno |
Cat# 706-606-148; RRID: AB_2340477 |
| DAPI |
Sigma |
D9542 |
| Biological Samples |
|
|
| Fetal eyes |
Birth Defects Research Laboratory at the University of Washington |
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
|
|
| BMP4 |
R&D systems |
Cat# 314-BP-050 |
| Paraformaldehyde |
Electron Microscopy Sciences |
Cat# RT-15710 |
| Trizol |
Invitrogen |
Cat# 15596026 |
| Critical Commercial Assays |
|
|
| Chromium Single Cell 3′ v1/v2/v3 Platform |
10X Genomics |
N/A |
| Illumina 75 Cycle High Sequencing Kit |
Illumina |
#20024906 |
| Papain Dissociation Kit |
Worthington |
#LK003150
|
| Deposited Data |
|
|
| Single cell transcriptomic comparison of human fetal retina, hPSC-derived retinal organoids, and long-term retinal cultures |
This paper |
GEO: GSE142526
|
| Experimental Models: Cell Lines |
|
|
| H1-hESC |
WiCell |
RRID: CVCL_9771 |
| H7-BRN3-tdTomato, hESC |
WiCell (Sluch et al., 2017) |
RRID:CVCL_9772 |
| H9-NRLGFP, hESC |
WiCell (Phillips et al., 2018) |
RRID: CVCL_9773 |
| Software and Algorithms |
|
|
| Adobe Creative Suite 4 |
Adobe |
N/A |
| ImageJ |
NIH |
N/A |
| Microsoft Office 2013 |
Microsoft |
N/A |
| Monocle 2.99 R package |
Trapnell et al., 2014 |
https://github.com/cole-trapnell-lab/monocle-release |
| Slingshot 1.2.0 R package |
Street et al., 2018 |
https://bioconductor.org/packages/release/bioc/html/slingshot.html |
| Seurat 3.1.0 R package |
Stuart et al., 2019 |
https://github.com/satijalab/seurat |
| Seurat 2.3.4 R package |
Butler et al., 2018 |
https://github.com/satijalab/seurat |
| umap-learn 0.3.7 Python library |
Becht et al., 2018 |
https://github.com/lmcinnes/umap |
| Other |
|
|
| Deconstructing Retinal Organoids: single cell RNA-Seq reveals the cellular components of human pluripotent stem cell-derived retina |
Collin et al., 2019 |
GEO: GSE119893
|
| Generation, transcriptome profiling, and functional validation of single cells from cone-enriched human retinal organoids |
Kim et al., 2019 |
GEO: GSE119343
|
