|
| Status |
Public on Mar 29, 2018 |
| Title |
SIGAG8 |
| Sample type |
SRA |
| |
|
| Source name |
Lin_negative_cKit_positive_sample_39
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell type: Lin-cKit+
strain: C57BL/6J*^*KitW-41J/J
genotype: Kit mutant (W41/W41)
|
| Treatment protocol |
Samples were lineage depleted using EasySep™ Mouse Hematopoietic Progenitor Cell Isolation Kit (STEMCELL Technologies).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The femora, tibiae, and ilia of C57BL/6 mice of W41/W41 mice were crushed and the bone marrow cells were released and the red blood cells were lysed with ammonium chloride solution (STEMCELL Technologies). The cells were stained with the fluorophore-conjugated monoclonal antibodies, and sorted using an Influx cell sorter (BD Biosciences) equipped with five lasers. The cells were sorted into 1.5 ml tubes containing PBS + 2% FCS.
Sorted cells were harvested, resuspended in 0.04% BSA (Thermo Fisher) and counted. Cells were processed using the 10x Chromium™ Single Cell 3’ kit, following manufacturers instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads aligned to mm10 and processed using Cell Ranger 1.3
Counts extracted using R-package (library: cellrangerRkit_1.1.0)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Counts: Mapped read counts per gene, per cell. Column headers are cell barcodes.
|
| |
|
| Submission date |
Dec 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bertie Gottgens |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Cambridge
|
| Street address |
Jeffrey Cheah Biomedical Centre
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE107727 |
A single cell hematopoietic landscape resolves 8 lineage trajectories and defects in Kit mutant mice |
|
| Relations |
| BioSample |
SAMN08134912 |
| SRA |
SRX3445731 |
