|
| Status |
Public on Oct 01, 2023 |
| Title |
RUNX1-ETO_DMSO_KASUMI_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
t(8;21) RUNX1-ETO AML
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KASUMI-1 cell line
genotype: KASUMI-1_DMSO
chip antibody: AML1-ETO (Diagenode, C15310197)
|
| Treatment protocol |
DMSO treatment 24h
|
| Growth protocol |
Cells were grown in standard media with addition 10-20% FCS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
x-linking was performed with 1% Formaldehyde. Lysates were clarified from sonicated nuclei and chromatin proteins were isolated with antibodies.
ChIP-Seq libraries were prepared for sequencing using a TruSeq ChIP Sample Prep Kit (Illumina) and standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RUNX1-ETO_DMSO_KASUMI_ChIPSeq.bdg
ChIP-Seq
|
| Data processing |
Chip Seq pipeline: Adapter sequences were trimmed for all reads and mapped against mm10 reference genome using Bowtie2. Uniquely mapped, deduplicated reads were retained and peaks were called using MACS2.
RNA Seq pipeline: Rads were trimmed for adaptor sequence. Paired end reads were aligned to mm10 genome STAR version 2.4.0. To generate the bigwig file, we first extended each read to 200 bp along 5' end and generated count files using HTSeq.
ATACSeq pipeline: Adapter sequences were trimmed for all reads and mapped against mm10 reference genome using Bowtie2. Uniquely mapped reads were retained without deduplication and peaks were called using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: Txt files with HTSeq count columns for RNA Seq, bedGraph files for ChIP Seq and ATAC-Seq
|
| |
|
| Submission date |
Feb 21, 2021 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Daniel Sasca |
| E-mail(s) |
danielsasca@gmail.com
|
| Organization name |
University Medical Center Mainz
|
| Department |
Department of Hematology and Oncology
|
| Street address |
Langenbeckstr 1
|
| City |
Mainz |
| ZIP/Postal code |
55131 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE167163 |
Acute resistance to BET inhibitors remodels compensatory transcriptional programmes via p300 co-activation |
|
| Relations |
| BioSample |
SAMN18021520 |
| SRA |
SRX10144598 |
