|
Status |
Public on Feb 09, 2012 |
Title |
FH-RYBP.HA |
Sample type |
SRA |
|
|
Source name |
293T-Rex, FH-RYBP.HA ChIP
|
Organism |
Homo sapiens |
Characteristics |
cell line: 293T-Rex transgene: Flag-HA-RYBP chip antibody: HA chip antibody vendor: Abcam chip antibody catalog #: ab9110 chip antibody lot: GR20600-2
|
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.PRC1.3
|
Data processing |
293Trex_FH-RYBP.HA.v2m1hg19f.bed.gz; genome build: hg19 293Trex_FH-RYBP.HA.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 |
SRX113580 |
BioSample |
SAMN00769170 |