|
Status |
Public on Dec 01, 2020 |
Title |
HT EZH2 |
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 #: 5246 chip antibody: EZH2
|
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 |
SRX181451 |
BioSample |
SAMN01141422 |