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Sample GSM1976952 Query DataSets for GSM1976952
Status Public on Mar 02, 2016
Title PAL-R
Sample type SRA
 
Source name lymphoid tissue
Organism Mus musculus
Characteristics cell type: Resting B cells from the spleen
passages: Sorted (CD43 negative) primary cells
strain: mixed background 129/C58BL/6
genotype: homozygous 3'PAL KO animals, unpublished at this time
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using miRNeasy kit (Qiagen) from either freshly purified splenic B cells, obtained after gradient separation using Lympholyte Mammal (Cedarlane) followed by CD43 negative selection (Miltenyi Biotec), or from purified splenic B cells stimulated in vitro (106 cells m/L) for 48 hours in RMPI 1640 medium (Lonza) supplemented with 10% fetal calf serum (Lonza) and with 5µg/mL LPS (Cayla Invivogen), separated on a Lympholyte Mammal gradient. For each genotype (wt, 3’PALD/D, hs3b-4D/D, 3’RRD/D), RNA sample was prepared from a pool of equivalent numbers of purified B cells from 4 animals
1 µg of total RNA were depleted from ribosomal RNA, ligated, reverse transcribed and amplified (14 cycles) with the reagents from the truseq stranded total RNA kit (illumina). Libraries were quantified with the Bioanalyzer DNA 1000 Kit (Agilent). 4nM of libraries were then diluted and denatured according to the Illumina recommendations. Paired-end 150-bp reads were sequenced on an Illumina Nextseq 500 sequencer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing STAR_2.4.0a paired-end mapping versus mm10.
FeatureCounts transcripts quantification (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Mus_musculus.GRCm38.77 Ensembl GTF annotation file.
Kallisto v0.42.3 transcripts quantification with Ensembl release 79 GTF file.
Genome_build: mm10
Supplementary_files_format_and_content: featurecounts_table.txt: raw counts from featureCounts (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Mus_musculus.GRCm38.77 Ensembl GTF annotation file. Kallisto_estcounts_table.txt: estimate counts produce with kallisto v0.42.3 with Ensembl release 79 GTF file. Kallisto_tpm_table.txt: transcript counts per million produce with kallisto v0.42.3 with Ensembl release 79 GTF file. BigWig files has been generated using samtools to discriminate expression strand for paired-end reads then genomeCoverageBed and bedGraphToBigWig from bedtools 2 suite.
 
Submission date Dec 21, 2015
Last update date May 15, 2019
Contact name Kevin Lebrigand
Organization name IPMC/CNRS
Lab Functional Genomics Platform of Nice-Sophia-Antipolis, France.
Street address 660 route des lucioles
City Valbonne - Sophia-Antipolis
ZIP/Postal code 06560
Country France
 
Platform ID GPL19057
Series (1)
GSE76217 RNA-SEQ on resting (R) and stimulated (S) B cells from several IgH 3'RR mutant models
Relations
BioSample SAMN04359441
SRA SRX1494400

Supplementary file Size Download File type/resource
GSM1976952_PAL-R.neg.bw 104.6 Mb (ftp)(http) BW
GSM1976952_PAL-R.pos.bw 107.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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