Comment[ArrayExpressAccession]	E-GEOD-42878
MAGE-TAB Version	1.1								
Public Release Date	2012-12-13
Investigation Title	Pregnancy-induced gene expression and differentiation of mouse mammary epithelium are co-governed by Nuclear Factor IB (NFIB) and STAT5								
Comment[Submitted Name]	Pregnancy-induced gene expression and differentiation of mouse mammary epithelium are co-governed by Nuclear Factor IB (NFIB) and STAT5
Experiment Description	Cytokines control the expression of common and cell-specific genes through the transcription factor STAT5. In mammary tissue specifically, expression of approximately 570 genes is induced during pregnancy by prolactin through STAT5, which binds to putative regulatory sequences. We have now asked whether mammary-specific induction of these genes can be linked to the presence of additional transcription factors, which would act in concert with STAT5. RNA-seq analysis at parturition identified 370 genes that were under NFIB control. Notably, 75% of these genes, encoding proteins linked to the differentiation of mammary epithelium, were also regulated by STAT5. This study demonstrates that the STAT5-NFIB module is an essential part of genes that define differentiation and function of the mammary gland. Expression profiling by high throughput sequencing in wild-type (WT) and Nfib-null (KO) mammary gland tissues								
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	Kang	Tang	Kang	Yoo	Zhu	Yamaji	Gronostajski	Robinson	Hennighausen
Person First Name	Keunsoo	Yong	Keunsoo	Kyung	Bingmei	Daisuke	Richard	Gertraud	Lothar
Person Mid Initials				H			M		
Person Email	kangk2@niddk.nih.gov								
Person Affiliation	NIH								
Person Phone	301-435-6636								
Person Address	NIDDK, NIH, 9000 Rockville Pike, Bethesda, MD, USA								
Person Roles	submitter								
Protocol Name	P-GSE42878-1	P-GSE42878-2							
Protocol Description	Mammary tissues without lymph nodes from mice of each genotype were collected, frozen in liquid nitrogen, and stored at -80 °C. Total RNA was extracted using TRIzol reagent, followed by a cleanup step using the RNeasy Plus Mini Kit (QIAGEN). Poly(A) RNA was purified twice from 1 mg total RNA and cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA), and sequenced using HiSeq 2000 (Illumina) RNA libraries were prepared for sequencing using standard Illumina protocols	Basecalls performed using the CASAVA software Sequenced reads were aligned to the mm9 genome assembly using the TopHat program (Trapnell et al., Bioinformatics, 2009) In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted. RPKM (reads per kilobase of transcript per million mapped reads) were calculated using a protocol (Mortazavi et al., Nat. Methods, 2008). Genome_build: mm9 Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.							
Protocol Type	nucleic acid library construction protocol	feature_extraction							
Experimental Factor Name	VARIATION								
Experimental Factor Type	variation								
Comment[SecondaryAccession]	GSE42878								
Comment[GEOReleaseDate]	2012-12-13								
Comment[ArrayExpressSubmissionDate]	2012-12-12								
Comment[GEOLastUpdateDate]	2012-12-14								
Comment[AEExperimentType]	RNA-seq of coding RNA								
Comment[AdditionalFile:Data1]	GSE42878_RPKM.txt								
Comment[SecondaryAccession]	SRP017526								
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR630862-SRR630866								
SDRF File	E-GEOD-42878.sdrf.txt