Comment[GEAAccession]	E-GEAD-949
MAGE-TAB Version	1.1
Investigation Title	Genome-wide analysis of EGR-1 binding sites (CBX71)
Experiment Description	We performed ChIP-chip analysis for EGR-1 in PMA stimulated THP-1 cells (1 hour after starting the stimulation). This analysis was performed in two independent biological replicates and three technical replicates for each samples.
Experimental Design	binding site identification design
Experimental Factor Name	sample_name
Experimental Factor Type	sample_name
Person Last Name	Kubosaki	Suzuki	Hayashizaki
Person First Name	Atsutaka	Harukazu	Yoshihide
Person Affiliation	Omics Science Center (OSC),RIKEN		
Person Roles	submitter		
Public Release Date	2025-01-31
Protocol Name	P-GEAD-3882	P-GEAD-3883	P-GEAD-3884	P-GEAD-3885	P-GEAD-3886	P-GEAD-3887	P-GEAD-3888	P-GEAD-3889
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol	growth protocol	treatment protocol
Protocol Description	The Human Promoter Array is a single array comprised of over 4.6 million probes tiled through over 25,500 human promoter regions. Sequences used in the design of the Human Promoter array were selected from NCbI human genome assembly (build 34). Repetitive elements were removed by RepeatMasker., Cel files were generated using Affymetrix's GCOS software and analyzed using the Affymetrix TAS analysis software. A P-value was computed at each probe position by assessing the excess of signal intensities detected by probes located within +/- 200 bp in the treatment relative to the control sample by wilcoxon rank sum test. The genome coordinates of the 25-mer probes, originally based on the version hg16 of human genome, were converted to hg18. The positions of the probes on hg18 were determined by aligning the probe sequences to the human genome (hg18) using Vmatch (http://www.vmatch.de).	none	none	Affymetrix fluidics protocol EukGE-WS2v4_450.	Scanning was carried out on an Affymetrix scanner GCS3000. The scan protocol was contained in a .cif file for chip type Hs_PromPR_v01., Affymetrix GCOS processed image files to generate .CEL files.	The intensities in the cel file were linearly scaled so that median intensity value is equal to the 500. The scaled data were normalized using quantile normalization. The normalization was achieved in both treatment and control groups together.	none	none
SDRF File	E-GEAD-949.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEAD-154
Comment[AEExperimentType]	transcription profiling by array
Comment[SecondaryAccession]	CBX71
Comment[BioProject]	PRJDB20048
Comment[CIBEX Accept Date]	2010-01-01
Comment[CIBEX Public Release Date]	2009-09-03
Comment[Last Update Date]	2025-01-31