|
| Status |
Public on Apr 27, 2020 |
| Title |
E9.5 HE replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
dissociated mouse embryos
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6C3F1/J + C57BL6/J
developmental stage: Embryonic day 9.5
genotype: wild type
marker: CD41- CD45- Kitlo/- CD31+ Runx1:GFP+
tissue: dorsal aorta plus umbilical and vitelline arteries
|
| Treatment protocol |
Females were superovulated by administering 5 IU of Pregnant Mare Serum Gonadotrophin and 5 IU human chorionic gonadotrophip at 48 and 0 hours prior to paring with males. Embryos were harvested at the appropriate embryonic day and cells were sorted on the same day as harvest.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were sorted into IMDM/10-20% FBS. Using the Chromium controller (10x Genomics) and reagents from the Chromium Single Cell 3′ Reagent Kit v2 (10x Genomics), cells were partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs) where each cell's trascriptome was indexed with a specific 10x BarCode. cDNA were amplified and purified for library preparation.
cDNA were used for library preparation using the Chromium Single Cell 3′ Reagent Kit v2 (10x Genomics) according to manufacturer’s protocol (CG00052, Rev D).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
10X sc-RNA-seq with cells from dissociated mouse embryos
|
| Data processing |
Data was processed using the 10X Genomics CellRanger pipeline. Sequencing reads were mapped to mm10 reference genome.
Filtering was performed on the raw gene-barcode matrix output by the Cell Ranger cellranger count function, removing barcodes that have fewer than 1000 transcripts and 1000 expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: gene_by_cell_count_matrix.txt contains a sparse matrix where rows are genes (with gene information in the gene_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are background corrected UMI counts for the given gene in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode, cell type, etc.) for each cell. gene_annotation.csv contains a data frame with gene id and gene short name.
|
| |
|
| Submission date |
Sep 09, 2019 |
| Last update date |
Apr 27, 2020 |
| Contact name |
Qin Zhu |
| Organization name |
UCSF
|
| Street address |
600 Minnesota Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94107 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE137116 |
Developmental trajectory of pre-hematopoietic stem cell formation from endothelium (scRNA-seq data set) |
| GSE137117 |
Developmental trajectory of pre-hematopoietic stem cell formation from endothelium |
|
| Relations |
| BioSample |
SAMN12716094 |
| SRA |
SRX6820191 |
