Comment[GEAAccession]	E-GEAD-301
MAGE-TAB Version	1.1
Investigation Title	Comparison of gene expression profiles between Parp-1+/+ and Parp-1-/- cells and livers
Experiment Description	Many lines of evidence suggest that poly(ADP-ribose) polymerase-1 (Parp-1) is involved in transcriptional regulation of various genes as a coactivator or a corepressor by modulating chromatin structure.  However, the impact of Parp-1-deficiency on the regulation of genome-wide gene expression has not been fully studied yet. We employed a microarray analysis covering 12,488 genes and ESTs using mouse Parp-1-deficient (Parp-1-/-) embryonic stem (ES) cell lines, primary embryonic fibroblasts (PMEF), and the livers of Parp-1-/- mice and their wild-type (Parp-1+/+) counterparts.
Experimental Design	genetic modification design
Experimental Factor Name	genotype
Experimental Factor Type	genotype
Person Last Name	Ogino	Masutani
Person First Name	Hideki	Mitsuko
Person Affiliation	ADP-ribosylation in Oncology Project, National Cancer Center Research Institute	
Person Roles	submitter	submitter
Public Release Date	2019-02-04
PubMed ID	17286852
Protocol Name	P-GEAD-124	P-GEAD-125	P-GEAD-126	P-GEAD-127	P-GEAD-128	P-GEAD-129	P-GEAD-130
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
Protocol Description	Parp-1-/- ES cell clones, 210-58 and 226-47, established independently from Parp-1+/- ES cell clones, 210 and 226, respectively, were used. They were all derived from male J1 ES cells.  The ES cell lines were maintained in Dulbecco's modified Eagle's medium (Invitrogen) containing 20% fetal calf serum supplemented with amino acids and leukemia inhibitory factor (LIF), ESGRO (Chemicon) in the absence of a STO feeder. The livers were prepared from Parp-1+/+ and Parp-1-/- female mice at 13 months of age, and about one-fifth of the amount of livers was used for total RNA extraction. Primary mouse embryonic fibroblasts (EFs) were derived from embryos at day 13.5 obtained by sister-brother mating of Parp-1+/- mice with a 129Sv/ICR mixed genetic background.  Briefly, each embryo was minced, trypsinized, and dispersed cells were incubated for 1 or 2 days until the EF cells became confluent.   The EF cells were replated on four dishes and when they became confluent, these EF cells were defined to be at the 3 population doubling level (PDL).  When the EF cells reached 6 PDL, they were harvested when they reached half confluency.	Total RNA was extracted from ES cells, the livers, and EF cells using Isogen (Nippon Gene).  Fifty micrograms of total RNA were treated with 5 units of DNase I (Invitrogen) for 15 min at room temperature, and purified again with Isogen. 5 ug of total RNA sample treated with DNase I were reverse-transcribed by Superscript II reverse transcriptase (Invitrogen) using T7-(dT)24 primer containing T7 RNA polymerase promoter sequence.	Total RNA was extracted from ES cells, the livers, and EF cells using Isogen (Nippon Gene).  Fifty micrograms of total RNA were treated with 5 units of DNase I (Invitrogen) for 15 min at room temperature, and purified again with Isogen. 5 ug of total RNA sample treated with DNase I were reverse-transcribed by Superscript II reverse transcriptase (Invitrogen) using T7-(dT)24 primer containing T7 RNA polymerase promoter sequence.	Total RNA was extracted from ES cells, the livers, and EF cells using Isogen (Nippon Gene).  Fifty micrograms of total RNA were treated with 5 units of DNase I (Invitrogen) for 15 min at room temperature, and purified again with Isogen. 5 ug of total RNA sample treated with DNase I were reverse-transcribed by Superscript II reverse transcriptase (Invitrogen) using T7-(dT)24 primer containing T7 RNA polymerase promoter sequence.	By using Affymetrix Microarray Suite software (Affymetrix).  The average fluorescence intensity was normalized by global scaling to 1,000.  The data were saved in Microsoft Excel files.	Per Chip normalization to the 50th percentile and Per Gene normalization to median by using GeneSpring 6.1 an d GX 7.3.1 software (Silicon Genetics). less than 0.0 to 0.0 by using GeneSpring 6.1 and GX 7.3.1 software (Silicon Genetics).	Parp-1-/- ES cell clones, 210-58 and 226-47, established independently from Parp-1+/- ES cell clones, 210 and 226, respectively, were used.  They were all derived from male J1 ES cells.  The ES cell lines were maintained in Dulbecco's modified Eagle's medium (Invitrogen) containing 20% fetal calf serum supplemented with amino acids and leukemia inhibitory factor (LIF), ESGRO (Chemicon) in the absence of a STO feeder. The livers were prepared from Parp-1+/+ and Parp-1-/- female mice at 13 months of age, and about one-fifth of the amount of livers was used for total RNA extraction. Primary mouse embryonic fibroblasts (EFs) were derived from embryos at day 13.5 obtained by sister-brother mating of Parp-1+/- mice with a 129Sv/ICR mixed genetic background.  Briefly, each embryo was minced, trypsinized, and dispersed cells were incubated for 1 or 2 days until the EF cells became confluent.   The EF cells were replated on four dishes and when they became confluent, these EF cells were defined to be at the 3 population doubling level (PDL).  When the EF cells reached 6 PDL, they were harvested when they reached half confluency.
SDRF File	E-GEAD-301.sdrf.txt
Comment[Number of channel]	single-channel
Comment[CIBEX Submitter]	Hideki Ogino, Mitsuko Masutani
Comment[Array Design REF]	A-AFFY-6
Comment[AEExperimentType]	transcription profiling by array
Comment[SecondaryAccession]	CBX22
Comment[BioProject]	PRJDB7987
Comment[CIBEX Accept Date]	2007-05-08
Comment[CIBEX Public Release Date]	2007-10-23
Comment[Last Update Date]	2019-08-14