|
| Status |
Public on Sep 24, 2020 |
| Title |
Input T_ALL3 ChIPmentation |
| Sample type |
SRA |
| |
|
| Source name |
PDX derived T-ALL blasts
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PDX derived T-ALL blasts
cosme subgroup: COSMe_I
antibody: none
patient_id: T_ALL3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50-100 000 CD45+ sorted, fixed cells were lysed in lysis buffer complemented with 20mM NaBU HDAC inhibitor and sheared on the Bioruptor Pico (Diagenode). Sheared chromatin was magnetically immunoprecipitated and tagmentated using the Auto ChIPmentation Kit for Histones (Diagenode).
Libraries were constructed with the Auto ChIPmentation Kit for histones (Diagenode). Libraries were sequenced with the Nextseq500 (SR75, High Output).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: ChIPmentation
Reads were trimmed by Trimmomatic and aligned to the reference genome hg38 with Bowtie2.
Peaks were called with MACS2 with the respective input control for each donor pool. Options for MACS2 were set to --extsize 73 –nomodel –broad
A matrix containing all significant peaks was made as reference for counting reads from BAM files using the function summarizeOverlaps from the R package GenomicAlignments.
Normalization of counts was done using DESeq2
Genome_build: hg38
|
| |
|
| Submission date |
Jul 29, 2020 |
| Last update date |
Sep 24, 2020 |
| Contact name |
Juliette Roels |
| E-mail(s) |
roels.juliette@gene.com
|
| Phone |
6505807476
|
| Organization name |
Genentech
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE155332 |
Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [ChIPmentation_TALL] |
| GSE155339 |
Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN15666524 |
| SRA |
SRX8842776 |
