|
| Status |
Public on Feb 09, 2012 |
| Title |
H3K27me3 |
| Sample type |
SRA |
| |
|
| Source name |
293T-Rex, H3K27me3 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 293T-Rex
transgene: Flag-HA (empty vector)
chip antibody: H3K27me3
chip antibody vendor: Millipore
chip antibody catalog #: 07-449
chip antibody lot: DAM1764447
|
| Treatment protocol |
Expression of the transgenes was induced by doxycycline treatment for 24 hours.
|
| Growth protocol |
293T-REx stable lines transfected with HA-tagged PRC1 subunits or an empty vector were grown in standard conditions (DMEM 10% FBS) and kept in selection with zeocin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to the manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
111219.RB.PRC1.10
|
| Data processing |
293Trex_FH.H3K27me3.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH.H3K27me3.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.
Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.
|
| |
|
| Submission date |
Dec 29, 2011 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Roberto Bonasio |
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Bonasio
|
| Street address |
3400 Civic Center Blvd - SCTR 9-111
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE34774 |
PCGF Homologs and RYBP Define Functionally Distinct PRC1 Family Complexes |
|
| Relations |
| SRA |
SRX113587 |
| BioSample |
SAMN00769177 |
