|
| Status |
Public on Oct 05, 2023 |
| Title |
DAMI-H3 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
DAMI cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DAMI cell
cell type: leukemic cells
disease state: MPN/AML
chip antibody: H3 (Abcam 1791)
|
| Growth protocol |
DAMI cells (ATCC, CRL-9792) were cultured in RPMI 1640 medium (Corning) supplemented with 10% fetal bovine serum (Sigma).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Bowtie2.2.1 was used for mapping the paired end reads to the hg19 human reference genome. Default parameters were used.
Samtools0.1.19 was used to convert, sort and index SAM files.
MACS2.1.1 was used to call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files were obtained from MACS2 in bed format
|
| |
|
| Submission date |
Nov 25, 2021 |
| Last update date |
Oct 05, 2023 |
| Contact name |
Linda M.S. Resar |
| Organization name |
Johns Hopkins University
|
| Department |
Department of Medicine / Division of Hematology
|
| Street address |
720 Rutland Avenue
|
| City |
BALTIMORE |
| State/province |
Maryland |
| ZIP/Postal code |
21210 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE189569 |
HMGA1 Chromatin Regulators Drive MPN Progression [ChIP-Seq] |
| GSE189570 |
HMGA1 Chromatin Regulators Drive MPN Progression |
|
| Relations |
| BioSample |
SAMN23440790 |
| SRA |
SRX13228292 |
