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Status |
Public on Jan 14, 2022 |
Title |
cd41:GFPlow-WT 2.5dpf |
Sample type |
SRA |
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Source name |
sorted cd41:GFPlow
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Organism |
Danio rerio |
Characteristics |
strain: EK genotype/variation: WT- tg(cd41:GFP) age: 2.5 dpf cell subset: sorted cd41:GFPlow
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 550 |
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Description |
SC1.A7-WT
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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
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Submission date |
Sep 16, 2020 |
Last update date |
Jan 15, 2022 |
Contact name |
Kai Yu |
E-mail(s) |
kai.yu@nih.gov
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Organization name |
NHGRI
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Street address |
50 South Drive, Bldg 50, Room 5151
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City |
Bethesda |
State/province |
Maryland |
ZIP/Postal code |
20892 |
Country |
USA |
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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 |
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Relations |
BioSample |
SAMN16191101 |
SRA |
SRX9139723 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4792208_SC1.A7-WT.barcodes.tsv.gz |
9.8 Kb |
(ftp)(http) |
TSV |
GSM4792208_SC1.A7-WT.genes.tsv.gz |
216.2 Kb |
(ftp)(http) |
TSV |
GSM4792208_SC1.A7-WT.matrix.mtx.gz |
12.8 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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