|
| Status |
Public on Feb 16, 2021 |
| Title |
KMS11_ChIP_Input |
| Sample type |
SRA |
| |
|
| Source name |
KMS11
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KMS11
cell type: Multiple Myeloma cell line
chip antibody: none (WCE)
|
| Treatment protocol |
Multiple myeloma cell lines were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.
|
| Growth protocol |
Daudi, RAJI, H929, JJN3, KMS11, KMS12, KMS28BM, RPMI-8226 and U266 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction from the H3K27ac ChIP-seq samples and sequencing of single-end 50bps long reads by the Illumina HiSeq 4000 were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Single end ChIP-Seq sequencing
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
ChIP-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were remove duplicate with samtools rmdup package.
ChIP-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is q-value < 0.01, keep-dup=1
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak files called with MACS2
|
| |
|
| Submission date |
Feb 25, 2020 |
| Last update date |
Feb 16, 2021 |
| Contact name |
Tze King Tan |
| Organization name |
National University of Singapore
|
| Department |
Cancer Science Institute
|
| Lab |
Takaomi Sanda Lab
|
| Street address |
14 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE145890 |
H3K27ac ChIP-seq for multiple myeloma cell lines, B-lymphoma cells and normal plasma cell |
| GSE145938 |
Super-enhancer profiling combined with CDK7 inhibition-transcripts identifies novel oncogenes of multiple myeloma. |
|
| Relations |
| BioSample |
SAMN14206170 |
| SRA |
SRX7798956 |
