|
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.
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|
|
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.
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|
|
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 |