|
| Status |
Public on Jul 28, 2020 |
| Title |
Input ChIPseq of Bone marrow mononuclear cells from AML patient – DMSO control [JCT19_DMSO_Input] |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Acute myeloid leukemia (AML)
patient: JCT19
cell type: Bone marrow mononuclear cells
treatment: DMSO
chip antibody: None
|
| Treatment protocol |
Each patient sample was divided into two groups, one treated with DAC (500 nM) for 72 hours and the other group (control) treated with DMSO.
|
| Growth protocol |
Cells were cultured in RPMI medium supplemented with 10% FBS for 24 hours prior to the experiment in a humidified incubator with 5% carbon dioxide supply.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-Seq libraries were prepared using SMARTer ThruPLEX DNA-seq kit (Takara Bio USA, Mountain View, CA) according to the manufacturer’s instructions.
1 to 2 ng fragmented double stranded DNAs were used to construct libraries with dual indices.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
JCT19_DMSO_Input
Bone marrow mononuclear cells of AML patient (Cleveland Clinic).
|
| Data processing |
Sequence reads were quality checked using FastQC v0.11.5, and the adapter sequences were removed and low quality (<20) bases at 3-prime ends were trimmed using Trim-galore v0.4.4.
Reads were then aligned to the reference human genome (hg38) using Bowtie v2.3.4.1 in an end-to-end alignment mode with default parameters.
Alignments with average phred quality score of < 10, PCR duplicates and those aligning to blacklisted regions of the genome were filtered out using Samtools v1.4.1.
The alignments were converted to bed format using bamtools v2.3.0 and the H3K9ac enriched (peak) regions were identified using diffReps v1.55.6 software with default parameters, using the input samples for background correction.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Bed format alignment files for each sample.
Supplementary_files_format_and_content: Tab-delimited text format differential peaks and hotspot regions for H3K9ac levels between DAC and DMSO.
|
| |
|
| Submission date |
Jun 18, 2020 |
| Last update date |
Jul 29, 2020 |
| Contact name |
Sridhar A Malkaram |
| E-mail(s) |
[email protected]
|
| Organization name |
West Virginia State University
|
| Department |
Mathematics and Computer Sciences
|
| Lab |
Marshall University Genomics and Bioinformatics Core
|
| Street address |
Barron Drive
|
| City |
Institute |
| State/province |
West Virginia |
| ZIP/Postal code |
25112 |
| Country |
USA |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE152804 |
Activation of SIRT6 by DNA hypomethylating agents and clinical consequences on combination therapy in leukemia |
|
| Relations |
| BioSample |
SAMN15318841 |
| SRA |
SRX8576860 |
