|
| Status |
Public on Dec 07, 2020 |
| Title |
AS-336708-LR-42261 |
| Sample type |
SRA |
| |
|
| Source name |
B220 sorted Myc-transgenic lymphoma cells transduced with MYD88-L265P;sh-scrambled (MSCV-GFP)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Myc upregulated lymphoma
tranduced with myd88-l265p in mscv-gfp: MYD88-L265P
knockdown: sh-scrambled control
|
| 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-scrambled (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 |
SAMN13480498 |
| SRA |
SRX7267426 |
