|
| Status |
Public on Oct 12, 2012 |
| Title |
H3K27me3_KARPAS-422 |
| Sample type |
SRA |
| |
|
| Source name |
KARPAS-422
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KARPAS-422
genotype/variation: EZH2 mutant
average gic50: 232 nM
chip antibody: anti-H3K27me3
chip antibody vendor: Millipore
chip antibody cat. #: 07-449
chip antibody lot #: DAM1662421
|
| Treatment protocol |
Cells were fixed for 15 minutes at room temperature with freshly prepared formaldehyde solution (final concentrations 1% formaldehyde, 10 mM NaCl, 0.1 mM EDTA pH 8.0, 5 mM HEPES pH 7.9) followed by the addition of glycine to 125mM. Fixed cells were rinsed twice in PBS containing 0.5% Igepal CA-630 (Sigma) and cell pellets were flash frozen. ChIP assays were performed using a custom assay protocol (ActiveMotif Inc.,San Diego, CA).
|
| Growth protocol |
Cells (5x10^7) were maintained in the appropriate cell culture media for 24 hours prior to fixation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted from formaldehyde-crosslinked cells and ChIP-ed using anti-H3K27me3 antibody Millipore 07-449 (lot# DAM1662421). ChIP DNA was processed into library by following the Illumina ChIP-Seq library construction protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Sample 3
|
| Data processing |
Fastq sequence files were aligned to the human reference (build hg19) using Bowtie allowing upto 2 mismatches. Only uniquely mapped reads were used for subsequent analysis.
Peaks of H3K27me3 enrichment were identified using SICER with optimized parameters and taking the corresponding Input sample as control; Fragment size of 250, Window size 750 bp and Gap size 2250 bp was used for calling peaks with SICER (were found to be optimal parameters after running with multiple parameters). Duplicate reads were removed before peak calling by SICER.
Statistically significant peaks (FDR<0.001) enriched in the ChIP sample relative to its corresponding input sample were annotated for genomic location
Genome_build: hg19
Supplementary_files_format_and_content: Bed files generated by SICER
|
| |
|
| Submission date |
Sep 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gopinath Ganji |
| E-mail(s) |
gopi@gsk.com
|
| Organization name |
GSK
|
| Street address |
1250 South Collegeville Road
|
| City |
Collegeville |
| State/province |
PA |
| ZIP/Postal code |
19426 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE40970 |
ChIP-seq analysis of H3K27me3 histone modification in EZH2 mutant and wild type DLBCL cell lines |
| GSE40972 |
EZH2 Inhibition as a Therapeutic Strategy for Lymphoma with EZH2 Activating Mutations |
|
| Relations |
| SRA |
SRX188593 |
| BioSample |
SAMN01179337 |
