|
| Status |
Public on Dec 08, 2020 |
| Title |
KO_rep3_RRBS |
| Sample type |
SRA |
| |
|
| Source name |
thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
age: 21 weeks
genotype: DNMT1 fl/fl CD4-CRE
Sex: male
cell type: thymocytes
|
| Extracted molecule |
genomic DNA |
| 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 |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| 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).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
|
| |
|
| 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) |
| GSE162217 |
Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK driven lymphomagenesis [RRBS] |
| GSE162218 |
Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK driven lymphomagenesis |
|
| Relations |
| BioSample |
SAMN16929702 |
| SRA |
SRX9593365 |
