Comment[ArrayExpressAccession] E-GEOD-46137 MAGE-TAB Version 1.1 Public Release Date 2013-10-15 Investigation Title Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B Comment[Submitted Name] Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B 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 Rousseaux Person First Name Sophie Person Email sophie.rousseaux@ujf-grenoble.fr Person Affiliation INSERM-UJF Person Address INSERM-UJF, Bd de la Chantourne, La Tronche, France Person Roles submitter Protocol Name P-GSE46137-19 P-GSE46137-15 P-GSE46137-29 P-GSE46137-26 P-GSE46137-7 P-GSE46137-30 P-GSE46137-23 P-GSE46137-9 P-GSE46137-39 P-GSE46137-25 P-GSE46137-17 P-GSE46137-16 P-GSE46137-40 P-GSE46137-10 P-GSE46137-36 P-GSE46137-14 P-GSE46137-34 P-GSE46137-3 P-GSE46137-11 P-GSE46137-6 P-GSE46137-13 P-GSE46137-22 P-GSE46137-32 P-GSE46137-42 P-GSE46137-21 P-GSE46137-18 P-GSE46137-4 P-GSE46137-43 P-GSE46137-33 P-GSE46137-44 P-GSE46137-2 P-GSE46137-24 P-GSE46137-38 P-GSE46137-8 P-GSE46137-27 P-GSE46137-31 P-GSE46137-5 P-GSE46137-1 P-GSE46137-37 P-GSE46137-28 P-GSE46137-12 P-GSE46137-20 P-GSE46137-41 P-GSE46137-35 P-GSE46137-48 P-GSE46137-49 P-GSE46137-45 P-GSE46137-51 P-GSE46137-47 P-GSE46137-46 P-GSE46137-50 Protocol Description The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R1_Rmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R3_Rplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_P5_Pplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_P2_Pplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P1_Pmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_P1_Pmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R5_Rmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P3_Pmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_R5_Rplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_P1_Pplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R5_Rplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R4_Rplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_R1_Rmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P4_Pmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_R2_Rplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R2_Rplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_P5_Pmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P3_Pplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P5_Pmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P6_Pplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R1_Rplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R4_Rmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_P3_Pmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_R3_Rmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R3_Rmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R6_Rplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P4_Pplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_R4_Rmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_P4_Pmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_R5_Rmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P2_Pplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R6_Rmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_R4_Rplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P2_Pmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_P3_Pplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_P2_Pmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P5_Pplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P1_Pplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_R3_Rplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_P4_Pplus.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_P6_Pmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2btag_R2_Rmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_R2_Rmoins.Detection Pval = The data were normalised using quantile normalisation. ID_REF = VALUE = quantile normalized th2bkd_R1_Rplus.Detection Pval = The starting amount of total RNA used for the reactions was 200 nanograms per sample. The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the manufacturer recommendations. Hybridization, staining and detection of cRNAs on Illumina Mouse WG-6 v2 Expression BeadChips were performed according to the manufacturer’s protocol. Spermatogenic cell suspensions from th2b+/tag mice were fractionated using a BSA gradient and pooled fraction of spermatocytes and round spermatids were used for ChIP with an anti-ha antibody exactly as previously reported in (Tan et al, 2011; PMID: 21925322). Total spermatogenic cell suspensions were prepared from wt mice and used for ChIP with an anti-TH2B antibody exactly as previously reported in (Tan et al, 2011; PMID: 21925322). 0.5-1 μg RNA was reverse transcribed with the SuperScriptTM III First-Strand Synthesis SuperMix (Invitrogen). Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Incorporation, Waltham, USA). Integrity of the extracted RNAs was assessed with the Bioanalyzer 2100 and the RNA6000 Nano kit (Agilent Technologies Incorporation, Santa Clara, USA). A RNA integrity number (RIN) greater or equal to 7.00 was achieved for all samples. Standard Applied Biosystems Life Technologies protocols were followed for the creation of short-insert bar-coded, paired-end libraries (insert length ~150 bp) according to the ChIP-seq Kit Guide from the manufacturer (cms_079323.pdf) and library preparation guide (cms_081748.pdf). The Illumina I-Scan system was used to scan Expression BeadChips, according to Illumina recommendations. Protocol Type normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol normalization data transformation protocol labelling protocol hybridization protocol sample treatment protocol sample treatment protocol nucleic acid library construction protocol nucleic acid library construction protocol array scanning protocol Experimental Factor Name GENOTYPE BRDT REPLICATE CHIP ANTIBODY CELL TYPE GENOTYPE Experimental Factor Type genotype brdt replicate chip antibody cell type genotype Comment[SecondaryAccession] GSE46137 Comment[GEOReleaseDate] 2013-10-15 Comment[ArrayExpressSubmissionDate] 2013-04-17 Comment[GEOLastUpdateDate] 2013-10-20 Comment[AEExperimentType] transcription profiling by array Comment[AEExperimentType] ChIP-seq SDRF File E-GEOD-46137.hyb.sdrf.txt E-GEOD-46137.seq.sdrf.txt