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Sample GSM2100954 Query DataSets for GSM2100954
Status Public on Nov 13, 2016
Title naive B cells replicate3
Sample type SRA
 
Source name lymphocytes_naive B cells
Organism Mus musculus
Characteristics strain: C57BL/6
Stage: 8 weeks after immunization
cell type: sorted B cells from spleen
cell subtype: naive B cells
Extracted molecule total RNA
Extraction protocol Spleen cells were isolated and all mononuclear cells were stained with a combination of antibodies (anti-CD19, anti-IgM, anti-IgG). Then subsets of memory B cells were sorted as CD19+HEL+YFP+IgM+ or IgG+ and naive cells as CD19+HEL+YFP-IgM+ using a FACSAriaIII flow cytometer. The purity of the sorted populations varied from 90-95%.
Directional libraries were prepared using the TruSeq Stranded total RNA Sample preparation kit following the manufacturer’s instructions (Illumina). The libraries were quantified by fluorimetric measurements with the Qubit® dsDNA HS Assay Kit (ThermoFisher). 51-bp Single Read sequences were generated on the Hiseq2500 sequencer according to manufacturer’s instructions (Illumina). Sequences were demultiplexed using the Illumina pipeline (Gerald, included in CASAVA version 1.7) giving FASTQ formatted reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description AF9-Nai1
Data processing cleaning with clean_ngs (v 0.7)
alignment with tophat (v 1.4.1.1)
counting with htseq-count (v 0.6.1)
Genome_build: GRCm38 (Ensembl version 74)
Supplementary_files_format_and_content: Htseq-count file; txt file with name of gene and corresponding counting
 
Submission date Mar 29, 2016
Last update date May 15, 2019
Contact name Rachel Legendre
E-mail(s) rachel.legendre@pasteur.fr
Organization name Institut Pasteur
Department Research and Resource Center for Scientific Informatics
Lab Hub of Bioinformatics and Biostatistics
Street address 28, rue du docteur Roux
City Paris
ZIP/Postal code 75724
Country France
 
Platform ID GPL17021
Series (1)
GSE79672 Comparison of gene expression of memory B cells subpopulations
Relations
BioSample SAMN04589344
SRA SRX1668193

Supplementary file Size Download File type/resource
GSM2100954_AF9-Nai1.tophat-mm10_GRCm38_74.htseq.out.txt.gz 137.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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