|
| Status |
Public on Mar 01, 2014 |
| Title |
H3K36me3 ChIP-seq in KOPT-K1 |
| Sample type |
SRA |
| |
|
| Source name |
KOPT-K1 naïve cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KOPT-K1
cell type: T-cell acute lymphoblastic leukemia
treated with: vehicle (naïve)
chip antibody: H3K36me3
chip antibody vendor: Abcam
chip antibody cat. #: ab9050
chip antibody lot #: Lot 761748
|
| Treatment protocol |
Persister cells were established by treating DND-41 or KOPT-K1 cells with 1 microM GSI for at least 7 weeks, replenishing the inhibitor every 3 - 4 days (Compound E, EMD4 Biosciences).
|
| Growth protocol |
The human T-cell leukemia cell lines DND-41 and KOPT-K1 were grown in RPMI 1640 containing 10% FCS at 37°C with 5% CO2. Cells were maintained between a density of 5 x 105 cells/ml and 2 x 106 cells/ml.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from formaldehyde-fixed cells (1 - 5 x 106 per histone mark, 107 for BRD4) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was isolated.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Cat #: FC-102-1001). Briefly, DNA was end-repaired using Epicentre’s End-it™ DNA-Repair Kit (Cat #: ER81050). The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of custom adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated using Angencourt® Ampure® XP. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
KOP_H3K36me3
|
| Data processing |
ChIP DNA and input controls were sequenced with the Hi-Seq Illumina Genome Analyzer.
ChIP-seq reads were aligned to the reference genome (hg19) using SOAP2 allowing at most two mismatches. Positions were randomly selected for reads with multiple hits. Reads aligned to the same position and strand were only counted once.
Aligned reads were extended by 250 bp to approximate fragment sizes and then a 25-bp resolution density map was derived by counting the number of fragments overlapping each position.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated in 25-bp step based on UCSC definition and converted into bigWig files using UCSC utilities.
|
| |
|
| Submission date |
Jan 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiang Zhu |
| E-mail(s) |
jzhu@mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital, Harvard Medical School and Broad Institute
|
| Lab |
Bradley Bernstein Lab
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE54379 |
Genome-wide chromatin maps of T-cell acute lymphoblastic leukemia (T-ALL) [ChIP-seq] |
| GSE54380 |
Genome-wide chromatin maps of T-cell acute lymphoblastic leukemia (T-ALL) |
|
| Relations |
| BioSample |
SAMN02595928 |
| SRA |
SRX448942 |
