Comment[ArrayExpressAccession]	E-GEOD-51714
MAGE-TAB Version	1.1									
Public Release Date	2014-11-14
Investigation Title	p53 activation effect on GM12878 lymphoblastoid cells									
Comment[Submitted Name]	p53 activation effect on GM12878 lymphoblastoid cells
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series									
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl								
Person Last Name	Wang									
Person First Name	Xuting									
Person Email	wang21@niehs.nih.gov									
Person Affiliation	NIEHS/NIH									
Person Phone	9193164598									
Person Address	NIEHS/NIH, 111 TW Alexander Dr, Research Triangle Park, NC, USA									
Person Roles	submitter									
Protocol Name	P-GSE51714-1	P-GSE51714-5	P-GSE51714-6	P-GSE51714-8	P-GSE51714-2	P-GSE51714-10	P-GSE51714-4	P-GSE51714-9	P-GSE51714-3	P-GSE51714-7
Protocol Description	Gene expression data were analyzed through Affymetrix Expression Console using gene-level RMA summarization and sketch-quantile normalization methods; core-gene analysis. ID_REF =  VALUE = RMA signal	Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).	Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the NIEHS Microarray Core Facility.	human lymphoblastoid cells were treated at a density of 900,000 cells/ml with 0.5 μM doxorubicin (Sigma) or water as a vehicle control for 18 hours	Lymphoblastoid cells were seeded at 15-cm dish and treated with 0.5 uM doxorubicin or vehicle (water) for up to 18h.	Lysates were clarified from sonicated nuclei and H3K4me3-DNA complexes were isolated with rabbit polyclonalanti-trimethyl-Histone H3 (Lys4) antibody (Millipore, cat# 07-473). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.	Total RNAs were extracted using Qiagen total RNA Miniprep kit (Qiagen, cat #74104 ) with DNase 1 (Invitrogen) digestion according to the manufacturer’s instructions.	human lymphoblastoid cells were grown as recommended by Coriell	Human lymphoblastoid GM12878 (Coriell Cell Repositories, Camden, NJ), were cultured in RPMI 1640 medium supplemented with 15% heat-inactivated fetal bovine serum (Invitrogen, Carlsbad, CA) and 1X antibiotics/antimycotics (Gibco, Carlsbad, CA). Cells were incubated at 37 C with 5% CO2.	Array scanning was performed according to the manufacturer's instruction (Affymetrix)
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	sample treatment protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol	growth protocol	array scanning protocol
Experimental Factor Name	time	compound								
Experimental Factor Type	time	compound								
Comment[SecondaryAccession]	GSE51714									
Comment[GEOReleaseDate]	2014-11-14									
Comment[ArrayExpressSubmissionDate]	2013-10-25									
Comment[GEOLastUpdateDate]	2014-11-18									
Comment[AEExperimentType]	transcription profiling by array									
Comment[AEExperimentType]	ChIP-seq									
SDRF File	E-GEOD-51714.hyb.sdrf.txt	E-GEOD-51714.seq.sdrf.txt