|
| Status |
Public on Nov 24, 2020 |
| Title |
N8: normal mouse Nestin low BMSC (V) |
| Sample type |
SRA |
| |
|
| Source name |
BM
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow stromal cells
cell population: Nestin low
cell type: normal
|
| Treatment protocol |
Bones were crushed in PBS with collagenase to get a cell suspension. After RBC lysis, cells were sortered as GFP+ CD45- CD31- DAPI-. Pellets were frozen at -80C to following obtain mRNA.
|
| Growth protocol |
Fresh mouse primary cells; leukemia was induced with doxycicline and mice were sacrificed once leukemia was evident due to high WBC in peripheric blood.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA was obtained using RNeasy kit (Qiagen).
As described in Picelli et al. Nat Protocols 2014; 171-181.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw reads were trimmed using trimGalore (version 0.4.1) and default options.
Trimmed reads were then aligned to the mm10 genome using Tophat2 (v2.1.0) and options "--no-coverage-search --read-mismatch 1 --max-multihits 1".
Genes were quantified with featurecounts (Liao et al., 2014) and options "-s 2 --primary -T 12 -Q 20 -t exon -g gene_id", using ensembl release 86 annotations.
Normalization and differential expression were performed using Deseq2 version 1.14.1.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts matrix with genes as rows and samples as columns
|
| |
|
| Submission date |
Nov 08, 2019 |
| Last update date |
Nov 24, 2020 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
data-submissions@stemcells.cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Wellcome-MRC Cambridge Stem Cell Institute
|
| Street address |
Puddicombe Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE140135 |
RNAseq for Nestin+ bone marrow stromal cells in normal and MLL-AF9 mice |
|
| Relations |
| BioSample |
SAMN13243065 |
| SRA |
SRX7119164 |
