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Sample GSM4154765 Query DataSets for GSM4154765
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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