Comment[GEAAccession]	E-GEAD-543
MAGE-TAB Version	1.1
Investigation Title	Genome-Wide Analysis of SP1 and SPI1 binding sites in THP-1
Experiment Description	We performed ChIP-chip analysis for SP1 and SPI1 (PU.1) in THP-1 cells and PMA stimulated THP-1 cells (96 hours 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	treatment
Experimental Factor Type	treatment
Person Last Name	Kasukawa
Person First Name	Takeya
Person Affiliation	RIKEN
Person Roles	submitter
Public Release Date	2022-09-27
PubMed ID	19377474
Protocol Name	P-GEAD-1434	P-GEAD-1435	P-GEAD-1436	P-GEAD-1437	P-GEAD-1438	P-GEAD-1439
Protocol Type	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol
Protocol Description	Affymetrix fluidics protocol EukGE-WS2v4_450.	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. 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. 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.	missing	missing	missing
SDRF File	E-GEAD-543.sdrf.txt
Comment[Number of channel]	single-channel
Comment[CIBEX Submitter]	Atsutaka Kubosaki, Hisashi Miura, Takahiro Suzuki, Shinji Kondo, Jun Kawai, Harukazu Suzuki, Yoshihide Hayashizaki, Katharine Irvine, Kate Schroder, David Hume
Comment[Array Design REF]	A-AFFY-86
Comment[AEExperimentType]	ChIP-chip by array
Comment[SecondaryAccession]	CBX43
Comment[BioProject]	PRJDB14407
Comment[CIBEX Accept Date]	2010-01-01
Comment[CIBEX Public Release Date]	2009-04-17
Comment[Last Update Date]	2022-09-28