|
Status |
Public on Nov 24, 2020 |
Title |
N6: normal mouse Nestin low BMSC (III) |
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 |
SAMN13243067 |
SRA |
SRX7119162 |