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Sample GSM4203319 Query DataSets for GSM4203319
Status Public on Dec 07, 2020
Title AS-336706-LR-42261
Sample type SRA
 
Source name B220 sorted Myc-transgenic lymphoma cells transduced with MYD88-L265P;sh-PDL1 (MSCV-GFP)
Organism Mus musculus
Characteristics tissue: Myc upregulated lymphoma
tranduced with myd88-l265p in mscv-gfp: MYD88-L265P
knockdown: knockdown of PD-L1
Extracted molecule total RNA
Extraction protocol RNA extraction was performed using Qiagen RNeasy+ kit (Qiagen) according manufacturer instructions.
Library was generated using SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) followed by Nextera XT Kit (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description mRNA single end RNAseq of Myc-transgenic lymphoma cells transduced with MYD88-L265P;sh-PDL1 (MSCV-GFP)
Data processing base-calling was performed according Illumina recommendations bcl2fastq-1.8.4.
50 bp single-end reads (Illumina) were aligned to reference genome mm10 and gtf.-transcriptome annotation release M7 (GENCODE) using STAR two-pass mode ( star 2.4.2a).
GENCODE M7 gtf.-file was used for quantification, performed by STAR (star 2.4.2a) , followed by normalisation, transformation and differential gene expression analysis in DEseq2 -1.12.4.
Genome_build: mm10
Supplementary_files_format_and_content: txt files include raw counts; normalized counts are available in files on series record.
 
Submission date Dec 04, 2019
Last update date Dec 07, 2020
Contact name Anna Dolnik
E-mail(s) anna.dolnik@charite.de
Organization name Charité Universitätsmedizin Berlin
Department Campus Virchow-Klinikum (CVK)
Lab Hämatologie, Onkologie und Tumorimmunologie
Street address Augustenburger Platz 1
City Berlin
ZIP/Postal code 13353
Country Germany
 
Platform ID GPL13112
Series (2)
GSE141452 DLBCL-reminiscent MyD88- or CARD11-mutant aggressive B-cell lymphomas exhibit strong pro-senescent and immune-evasive phenotypes [part1]
GSE141454 DLBCL-reminiscent MyD88- or CARD11-mutant aggressive B-cell lymphomas exhibit strong pro-senescent and immune-evasive phenotypes
Relations
BioSample SAMN13480506
SRA SRX7267418

Supplementary file Size Download File type/resource
GSM4203319_AS-336706-LR-42261.counts.txt.gz 187.0 Kb (ftp)(http) TXT
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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