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Sample GSM937858 Query DataSets for GSM937858
Status Public on Jul 02, 2014
Title 293Trex_N3.input
Sample type SRA
 
Source name 293T-Rex
Organism Homo sapiens
Characteristics cell line: 293T-Rex
transgene: N3 (empty vector)
epitope tag: Flag-HA-OneSTrEP (N-terminal)
antibody: none
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
K562 cells were grown in standard conditions (RPMI 10% FBS)
Extracted molecule genomic DNA
Extraction protocol Method for DNA: isolation of nuclei, lysis and sonication, IP, cross link reversal, qiaquick PCR purification column. Libraries were prepared according to 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
 
Data processing Trimmed (3') sequences to 40 nts
Mapped to hg19 using bowtie -v2 -m1
Duplicates were removed with samtools rmdup
Wig coverage was calculated with IGVtools extending the reads to 200 nts
Wigs were normalized to 10,000,000 sequenced reads using a shell script
Genome_build: hg19
Supplementary_files_format_and_content: Normalized WIGs
 
Submission date May 25, 2012
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 (2)
GSE38273 ChIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells
GSE38275 ChIP-seq and RIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells
Relations
SRA SRX149701
BioSample SAMN00998596

Supplementary file Size Download File type/resource
GSM937858_293Trex_N3.input.v2m1hg19fen.wig.gz 298.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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