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Sample GSM4432242 Query DataSets for GSM4432242
Status Public on Dec 08, 2020
Title B33-I
Sample type SRA
 
Source name activated B cell
Organism Mus musculus
Characteristics strain: C57BL/6
treatment: 33 hours after LPS treatment
Treatment protocol Naïve B cells were negatively isolated (Miltenyi, 130-090-862), CTV labelled and stimulated with 25μg/ml LPS (Salmonella typhosa origin, Sigma)
Growth protocol B lymphocytes were cultured in RPMI 1640 with 2mM GlutaMAX, 50 μM β-mercaptoethanol and 10% heat-inactivated fetal calf serum
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using NucleoSpin RNA Plus (Macherey-Nagel) from sorted naïve/activated/differentiated B cell populations
mRNA reverse transcription cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Base-calling was performed using Illumina Casava v1.8.2
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using Rsubread::align.
Genewise counts were obtained using featureCounts with Rsubread's inbuilt mm10 annotation.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text giving Entrez Gene IDs, gene length (number of bases in union of all exons) and the number of read-pairs assigned to that read.
 
Submission date Mar 24, 2020
Last update date Dec 08, 2020
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL19057
Series (2)
GSE147496 RNA-seq of primary mouse B cell progenitor populations after activation with LPS
GSE147497 RNA-seq and in situ Hi-C of primary mouse B cell progenitor populations after activation with LPS
Relations
BioSample SAMN14443806
SRA SRX7988773

Supplementary file Size Download File type/resource
GSM4432242_GenewiseCounts_B33-I.tsv.gz 178.5 Kb (ftp)(http) TSV
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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