GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM855016 Query DataSets for GSM855016
Status Public on Feb 09, 2012
Title H2AK119Ub1
Sample type SRA
Source name 293T-Rex, H2AK119Ub1 ChIP
Organism Homo sapiens
Characteristics cell line: 293T-Rex
transgene: Flag-HA (empty vector)
chip antibody: H2AK119Ub1
chip antibody vendor: Cell Signaling
chip antibody catalog #: 8240
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 HiSeq 2000
Description 111219.RB.PRC1.11
Data processing 293Trex_FH.H2AUb_cs.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH.H2AUb_cs.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 GPL11154
Series (1)
GSE34774 PCGF Homologs and RYBP Define Functionally Distinct PRC1 Family Complexes
SRA SRX113588
BioSample SAMN00769178

Supplementary file Size Download File type/resource
GSM855016_293Trex_FH.H2AUb_cs.v2m1hg19f.bed.gz 139.5 Mb (ftp)(http) BED
GSM855016_293Trex_FH.H2AUb_cs.v2m1hg19f.wig.gz 194.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap