NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1239074 Query DataSets for GSM1239074
Status Public on Sep 24, 2013
Title CBP ChIP-Seq for HSP70K71E_n2
Sample type SRA
 
Source name HEK293
Organism Homo sapiens
Characteristics cell line: Human Kidney Embryonic Cell line HEK293
genotype/variation: HSP70K71E-EGFP
chip antibody: anti-CBP [CBP/anti-KAT3A-chip grade, cat no. ab2832 ABCAM]
Growth protocol HEK293 cells and the cells expressing HSP70K71E were proliferated with RPMI1640, 10% FBS, 25 mM HEPES, 1X PS
Extracted molecule genomic DNA
Extraction protocol ChIP'd DNA was extracted accordingly in previous publication (Byun et al, ELL faciliates RNA polymerase II pause site entry and release. Nature Communications 3, 633 2012.
ChIP-Seq samples were sequenced on GAIIx with 36bp length using Illumina TruSeq v3 Chemistry, Allthe samples have good quality with over 93% of bases having Q30 or above. Library complexity is measured by uniquely aligned reads using picard's markduplicate utility.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description T1CBP
ChIP'd DNA
Data processing PhiX was used for sequencing control and illumina TruSeq V3 was used for sequencing chemistry.
The basic calling is analyzed by illumina RTA 1.8. 70.0 and allignment was used by illumina Casava 1.8.2
An unthresholded hotspot is determined as a contiguous union of 250 bp window whose z-scores are greater than 2.
Once a hotspot is called, the z-scoreof the hotspot is given by the maximum z-score of the constituent tags.
More detailed steps for ChIP-Seq data analysis were described in the manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files
 
Submission date Sep 24, 2013
Last update date May 15, 2019
Contact name Jung S Byun
E-mail(s) byunjs@mail.nih.gov
Phone 3014352890
Organization name NCI/NIH
Lab Genetics Branch
Street address 37 convent drive, Bldg 37, Rm 1042
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL10999
Series (2)
GSE51117 Genome wide ChIP-Seq profiles of p300 and CBP in control and cells expressing HSP70K71E
GSE51118 p300 is a preferred client protein for Nuclear Chaperones
Relations
BioSample SAMN02362718
SRA SRX359409

Supplementary file Size Download File type/resource
GSM1239074_T1CBP_n2.BEDGRAPH.gz 105.4 Mb (ftp)(http) BEDGRAPH
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