|
| Status |
Public on Dec 01, 2020 |
| Title |
HT H3K27me3 |
| Sample type |
SRA |
| |
|
| Source name |
Diffuse large B cell lymphoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HT
chip antibody manufacturer: Cell Signaling
chip antibody catalog #: 9733
chip antibody: H3K27me3
|
| Treatment protocol |
No treatment -- baseline measurement of methylation / occupancy without perturbation.
|
| Growth protocol |
HT and SUDHL6 cell lines were grown in Roswell Park Memorial Institute (RPMI) GlutaMAX medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Invitrogen).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
baseline measurement of methylation / occupancy without perturbation
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
The 36-nt sequence reads from Illumina's Genome Analyzer 2 were mapped to the genome using the ELAND algorithm. Only tags that mapped uniquely, had no more than 2 mismatches, and passed quality control filtering were used in the subsequent analysis.
Mapped reads were extended in silico at their 3' ends to a length of 140 bp, reflecting the average fragment length in the size selected library.
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain the output of applying SICER to each sample. WIG and TDF files were generating using IGVTools' count function on aligned sequence reads, assuming a fragment length of 200, and using a bin size of 25 nt for WIG and 10 nt for TDF files.
|
| |
|
| Submission date |
Aug 29, 2012 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Barbara M Bryant |
| E-mail(s) |
barbara.bryant@constellationpharma.com
|
| Organization name |
Constellation Pharmaceuticals
|
| Street address |
215 First Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE40472 |
Selective lymphoma cell killing by a PRC2 small molecule inhibitor (ChIP-Seq set 1) |
| GSE40476 |
Selective lymphoma cell killing by a PRC2 small molecule inhibitor |
|
| Relations |
| SRA |
SRX181449 |
| BioSample |
SAMN01141420 |
