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Sample GSM1264670 Query DataSets for GSM1264670
Status Public on Nov 17, 2013
Title Bcells_18hEstradiol_RNAseq
Sample type SRA
 
Source name primary Bcell after 18h treatment of estradiol
Organism Mus musculus
Characteristics cell type: primary B cells
treatment: Estradiol for 18h
Treatment protocol Cells were trypsinized and FACS-sorted to remove feeder and dead cells
Growth protocol ESCs and iPSCs were cultured on mitomycin C treated MEF feeder cells in KO-DMEM (Invitrogen) supplemented withL-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, 1,000 U/ml LIF (ESC medium) and 15% fetal bovine serum (FBS, Invitrogen). MEF cultures were established by trypsin digestion of mouse embryos (embryonic day 13.5) and the resulting cells cultured in DMEM supplemented with 10% FBS, L-glutamine and penicillin/streptomycin. CD19+ pro-B and pre-B cells were isolated from bone marrow using monoclonal antibodies to CD19 (1D3), obtained from BD Pharmingen, using MACS (Miltenyi Biotech). After isolation B cells were grown in RPMI medium supplemented with 10% FBS and IL-7. cell reprogramming experiments were conducted in gelatinized plates seeded with a feeder layer of the OP9 stromal cell line, using ESC medium supplemented with 2μg/ml of doxycycline and 15% FBS. For the reprogramming of B cells, IL-4 (10ng/ml), IL-7 (10ng/ml) and IL-15 (2ng/ml) were added to the medium.
Extracted molecule polyA RNA
Extraction protocol RNA isolation was done with the miRNeasy Mini kit
Libraries was prepared with the Truseq stranded mRNA protocol, with an insert size of 200 to 400bp.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sample 2
Data processing Basecalls: performed with Illumina's CASAVA-1.8.2 software
Reads alignement: performed with STAR v2.3.0.1 (option: outFilterMismatchNmax 2, outFilterMultimapNmax 1)
Reads counting: performed with Htseq count (option: mode union, stranded, features exons, attribute gene_id) on Refseq mm9 annotation
Filtering: genes for which no reads were counted in both conditions were removed before normalisation
Normalization: performed with Deseq (option: method blind, sharingMode fit-only, fitType local)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated file. Col1=gene Name; Col2=normalized reads count
 
Submission date Nov 14, 2013
Last update date May 15, 2019
Contact name Bruno Di Stefano
E-mail(s) distefanob@gmail.com
Organization name Harvard University
Department Harvard Dept. of Stem Cell and Regenerative Biology
Street address 185 Cambridge Street
City Boston
State/province Ma
ZIP/Postal code 02114
Country USA
 
Platform ID GPL13112
Series (2)
GSE52396 C/EBPα poises B cells for rapid reprogramming into iPS cells [RNA-Seq]
GSE52397 C/EBPα poises B cells for rapid reprogramming into iPS cells
Relations
Reanalyzed by GSE80797
BioSample SAMN02402776
SRA SRX377718

Supplementary file Size Download File type/resource
GSM1264670_RNAseq_Bcells_18hEOH_Normalized.tsv.gz 162.8 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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