|
| Status |
Public on Jun 07, 2023 |
| Title |
Rax-GFP ESCs, day 6, three biological replicate pool, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
ESC-derived eye organoids (Rax-GFP ESCs)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: eye organoid
cell type: retina progenitors
genotype: Rax-GFP knockin Het
treatment: culture day 6
|
| Growth protocol |
The method was descrived previously Nature Protocols volume 7, pages69–79 (2012).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Chromium Single Cell v2 Reagent Kit and Controller (10X Genomics, Pleasanton, CA, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Single cell data was further processed with Seurat, version 2.3.4
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Feb 06, 2023 |
| Last update date |
Jun 07, 2023 |
| Contact name |
NOZOMU TAKATA |
| E-mail(s) |
nozomu.takata@northwestern.edu
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Department |
Center for Vascular and Developmental Biology
|
| Street address |
303 East Superior Street, 10-220
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE202758 |
Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis [scRNA-seq] |
| GSE202759 |
Lactate-dependent Transcriptional Regulation Controls Mammalian Eye Morphogenesis. |
|
| Relations |
| BioSample |
SAMN33141964 |
| SRA |
SRX19293636 |
