|
| Status |
Public on Dec 08, 2020 |
| Title |
ALKKO_rep2_RNA |
| Sample type |
SRA |
| |
|
| Source name |
thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
age: 21 weeks
genotype: NPM-ALK+, DNMT1 fl/fl CD4-CRE
Sex: male
cell type: thymocytes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA and DNA were isolated using the QIAGEN AllPrep DNA/RNA mini isolation kit to enable simultaneous isolation of nucleic acids from the same specimen. Tissues were homogenized using EPPI-Mikropistills (Schuett-biotec) and RNA and DNA isolation was performed according to the manufacturer’s protocol. RNA and DNA were eluted in nuclease free ddH2O.
Standard Illumina protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 and 3.3.52 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.3 and 2.7.7.
BCL to BAM file conversion and demultiplexing with Illumina2bam 1.17 (http://wtsi-npg.github.io/illumina2bam/) and custom programmes based on Picard tools 2.19.2 (https://github.com/DanieleBarreca/picard/)
Reads were quality-controlled using fastQC (106) and pre-processed using trimgalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to trim adapter and low quality sequences.
Reads were aligned to mouse genome (mm10) and processed further using STAR (107).
Differential gene expression levels of the transcripts were quantified by HTSeq (108) and analyzed using the Bioconductor package DESeq2 (109).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file reports abundance measurements
|
| |
|
| Submission date |
Nov 26, 2020 |
| Last update date |
Dec 09, 2020 |
| Contact name |
Gerda Egger |
| E-mail(s) |
[email protected]
|
| Organization name |
Medical University of Vienna
|
| Department |
Pathology
|
| Street address |
Waehringer Guertel 18-20
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE162216 |
Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK driven lymphomagenesis [RNA-Seq] |
| GSE162218 |
Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK driven lymphomagenesis |
|
| Relations |
| BioSample |
SAMN16929673 |
| SRA |
SRX9593354 |
