|
| Status |
Public on Mar 22, 2021 |
| Title |
MM.1S_RNAPIISer5p_JQKD82_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
multiple myeloma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MM.1S
cell type: multiple myeloma cell line
treatment: 1 uM JQKD82 for 48h
chip antibody: Phospho-Rpb1 CTD (Ser5) (Cell signaling technology,13523, lot1)
|
| Growth protocol |
MM.1S cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MM.1S cells were crosslinked, lysed and sonicated. For ChIP with reference exogenous genome, spike-in chromatin (Active Motif, 53083) was then added. The protein-bound DNA fragments were then immunoprecipitated with specific antibodies. After reverse-crosslinking, DNA was purified using QIAquick PCR Purification Kit (Qiagen).
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were aligned to the reference human genome (hg19) using BWA.
ChIP-seq peaks were called using MACS2 (Model-Based Analysis of ChIP-seq) with p=1X10-7 in "narrow" mode.
ENCODE blacklisted regions were removed.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Peak files are BED files for each sample.
|
| |
|
| Submission date |
Apr 03, 2020 |
| Last update date |
Mar 22, 2021 |
| Contact name |
Hiroto Ohguchi |
| E-mail(s) |
ohguchi@kumamoto-u.ac.jp
|
| Phone |
+81-96-373-6596
|
| Organization name |
Kumamoto University
|
| Department |
IRDA
|
| Lab |
Ohguchi Lab
|
| Street address |
2-2-1 Honjo, Chuo-ku
|
| City |
Kumamoto |
| State/province |
Kumamoto |
| ZIP/Postal code |
860-0811 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE148046 |
ChIP-seq analyses for KDM5A, H3K4me3, RNAPII and TAF3 in human multiple myeloma cell line MM.1S |
| GSE148048 |
ChIP-seq and RNA-seq analyses in human multiple myeloma cell line MM.1S |
|
| Relations |
| BioSample |
SAMN14533581 |
| SRA |
SRX8053106 |
