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Sample GSM3227550 Query DataSets for GSM3227550
Status Public on Apr 19, 2019
Title pBIC_2
Sample type SRA
 
Source name B220+GFP+ cells from spleen
Organism Mus musculus
Characteristics murine model: ABC-DLBCL lymphoma (pBIC)
genotype/variation: pBIC, p53F/FBlimp1F/FIKK2castopF/stopFCg1Cre/+
cell type: splenic B cells (B220+GFP+)
Extracted molecule total RNA
Extraction protocol Murine spleens were submitted to cellular disaggregation, followed by lysis of erythrocytes using ACK buffer. Then, single-cell preparations were stained with B220 and submitted to fresh cellular sorting in a FACSAria Ilu sorter (BD) after exclusion of dead cells with 7AAD. Total RNA was extracted from sorted cells using TRIzol (Invitrogen) as described in manufacturer´s protocol and quality control of extracted RNA was measured using Agilent Bioanalyzer.
General transcriptome library preparation and massive sequencing were performed by BGI Tech (BGI, Shenzhen, China) using the Illumina HiSeq4000 platform with the paired-end 100-bp read option.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description PolyA RNA
Data processing The quality of the samples was verified using FastQC software.
FASTQ files were mapped to mm10 mouse assembly using STAR with default parameters.
featureCounts software and Gencode M13 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include gene counts obtained with featureCounts for each sample.
 
Submission date Jun 26, 2018
Last update date Apr 19, 2019
Contact name SERGIO ROA
E-mail(s) sroa@unav.es
Organization name University of Navarra
Department Biochemistry and Genetics
Lab Immunogenetics lab
Street address Irunlarrea, 1
City Pamplona
ZIP/Postal code 31008
Country Spain
 
Platform ID GPL21103
Series (2)
GSE116288 Transcriptional profiling of murine ABC-DLBCL-like tumors [RNA-seq]
GSE116290 PD-1/PD-L1 immune checkpoint and p53 loss facilitate tumor progression in activated B cell diffuse large B-cell lymphomas
Relations
BioSample SAMN09491341

Supplementary file Size Download File type/resource
GSM3227550_pBICh_2.counts.txt.gz 2.6 Mb (ftp)(http) TXT
Raw data are available in SRA
Processed data provided as supplementary file

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