|
| Status |
Public on Oct 29, 2024 |
| Title |
vehicle, early, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
timepoint: early
treatment: vehicle
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total ribonucleic acid (RNA) was extracted using the RNeasy® Micro kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol. RNA was eluted in RNase free water and stored at -80°C. RNA concentrations were determined using the NanoDrop spectrophotometer. For simultaneous isolation of total RNA and genomic DNA (and protein) for submission to RNA sequencing and whole exome sequencing of CD5+CD19+ FACS-sorted cell the AllPrep DNA/RNA/Protein Mini Kit was used according to manufacturer’s protocol.
Library preparation of RNA was performed according to the Illumina TruSeq Stranded protocol on a HiSeq 2000 v4 sequencer, paired-end 125 base pairs with five samples per lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
CLL_mouse5_tumor-v-er
|
| Data processing |
Raw sequencing reads from RNA sequencing were aligned with STAR (2.5.3a) and reads were counted per gene using featurecounts (1.5.3).
Assembly: GRCm38
Supplementary files format and content: bam Aligned reads
Supplementary files format and content: counts*.txt Featurecounts
|
| |
|
| Submission date |
Oct 13, 2022 |
| Last update date |
Oct 29, 2024 |
| Contact name |
Marc Zapatka |
| E-mail(s) |
m.zapatka@dkfz.de
|
| Organization name |
German Cancer Research Center
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| State/province |
Select State |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE215414 |
Longitudinal omics data followed by preclinical treatment studies identify proteasome inhibition as potential salvage strategy for ibrutinib-resistant CLL |
|
| Relations |
| BioSample |
SAMN31270001 |
| SRA |
SRX17878122 |
