|
| Status |
Public on Jan 14, 2022 |
| Title |
cd41:GFPlow-runx1-/- 10dpf |
| Sample type |
SRA |
| |
|
| Source name |
sorted cd41:GFPlow
|
| Organism |
Danio rerio |
| Characteristics |
strain: EK
genotype/variation: runx1-/- (del8, hg96)-tg(cd41:GFP)
age: 10 dpf
cell subset: sorted cd41:GFPlow
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium.
Single-cell RNA-seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis, cDNA preparation and library construction were prepared following the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
SC6.zf_rx1_10dpf_cd41
|
| Data processing |
Sequences from the Chromium platform were de-multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome (GRCz10) and transcript annotation reference (GRCz10.87) with default parameters.
Genome_build: GRCz10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, features.tsv, matrix.mtx
|
| |
|
| Submission date |
Sep 16, 2020 |
| Last update date |
Jan 15, 2022 |
| Contact name |
Kai Yu |
| E-mail(s) |
kai.yu@nih.gov
|
| Organization name |
NHGRI
|
| Street address |
50 South Drive, Bldg 50, Room 5151
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL25922 |
| Series (2) |
| GSE158099 |
Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development |
| GSE158101 |
Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development |
|
| Relations |
| BioSample |
SAMN16191096 |
| SRA |
SRX9139728 |
