|
| Status |
Public on Nov 27, 2023 |
| Title |
E11 AGM cells - NG2 +/+; Runx1 fl/fl (WT) |
| Sample type |
SRA |
| |
|
| Source name |
aorta-gonads-mesonephros region
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E11
genotype: NG2 +/+; Runx1 fl/fl (WT)
tissue: aorta-gonads-mesonephros region
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hematopoietic organs were dissected and dissociated into single cells with collagenase type I (Sigma, C0130, 0.12% v/v)
AGMs from NG2 +/+; Runx1 fl/fl and NG2-Cre; Runx1 fl/fl embryos were dissected, dissociated, washed, counted and assessed for viability using a Bio-Rad TC20. Cells were then loaded at a concentration for the recovery of 7,000 cells and processed through the 10x Chromium Controller. Single cell libraries were obtained according to manufacturer protocol. RNA concentration was obtained using Quibit RNA HS (Thermo-Fisher) and the quality of the libraries was verified using the LabChip GX24 (Perkin Elmer).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Alignment of scRNA-seq data and barcode counting using 10X Genomics Cell Ranger (v3.1.0) with reference dataset mm10/GRCm38-3.0.0.
Filtering of empty and/or low quality cells using EmptyDrops and Scater (v1.14.6) Bioconductor packages
Differential expression computed using the Scran (v1.14.6) Bioconductor package
Enrichment analysis of differential expression results and additional data mining of Gene Ontology terms with the Panther classification system and AmiGO (v2.5.13)
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain tab separated feature and barcode sequences corresponding to matrix row and column indices respectively, as output by 10X Cell Ranger
Supplementary_files_format_and_content: mtx files contain market exchange formatted matrices of UMI counts associated with a feature (row) and barcode (column), as output by 10X Cell Ranger
|
| |
|
| Submission date |
Jun 27, 2021 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Mihaela Crisan |
| E-mail(s) |
mihaela.crisan@ed.ac.uk
|
| Organization name |
The University of Edinburgh
|
| Street address |
5 Little France Drive
|
| City |
Edinburgh |
| ZIP/Postal code |
EH16 4UU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE178981 |
Runx1+ vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo |
|
| Relations |
| BioSample |
SAMN19903360 |
| SRA |
SRX11237386 |
