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Series GSE40948 Query DataSets for GSE40948
Status Public on Oct 21, 2012
Title Genome-wide nucleosome positioning during embryonic stem cell development [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We determined genome-wide nucleosome occupancy in mouse embryonic stem cells and their neural progenitor and embryonic fibroblast counterparts to assess features associated with nucleosome positioning during lineage commitment. Cell type and protein specific binding preferences of transcription factors to sites with either low (e.g. Myc, Klf4, Zfx) or high (e.g. Nanog, Oct4 and Sox2) nucleosome occupancy as well as complex patterns for CTCF were identified. Nucleosome depleted regions around transcription start and termination sites were broad and more pronounced for active genes, with distinct patterns for promoters classified according to their CpG-content or histone methylation marks. Throughout the genome nucleosome occupancy was dependent on the presence of certain histone methylation or acetylation modifications. In addition, the average nucleosome-repeat length increased during differentiation by 5-7 base pairs, with local variations for specific genomic regions. Our results reveal regulatory mechanisms of cell differentiation acting through nucleosome repositioning.
Overall design The Total RNA from ESCs, NPCs and MEFs was extracted by guanidinisothiocyanat/phenol extraction with the Trifast kit (Peqlab). Total RNA preparations were treated with DNase I, phenol/chloroform extracted and precipitated before further processing. RNAs were depleted of 5S, 5.8S, 18S and 28S rRNAs using the Human/Mouse/Rat Ribo-Zero rRNA Removal Kit (Epicentre) according to the manufacturer’s protocol. After rRNA depletion, RNAs were fragmented with a kit from Ambion. Libraries for Solexa sequencing were generated according to the standard Illumina protocol that comprised first strand cDNA synthesis, second strand cDNA synthesis, end repair, addition of a single A base, and adapter ligation. Sequencing was performed on the Illumina GAIIx (replicate 1) and Illumina HiSeq 2000 (replicate 2) platforms at the sequencing core facilities of the BioQuant in Heidelberg, Germany. RNA reads were aligned with TopHat. Further expression analysis was with the Genomatix software suite (Genomatix, Munich, Germany) and the Eldorado gene annotation. For each transcript a normalized expression value was calculated from the read distribution that accounts for the length differences using the program DEseq for the analysis of differential expression.
Contributor(s) Teif VB, Rippe K
Citation(s) 23085715
Submission date Sep 18, 2012
Last update date May 15, 2019
Contact name Vladimir B Teif
Organization name University of Essex
Department School of Life Sciences
Street address Wivenhoe Park
City Colchester
ZIP/Postal code CO4 3SQ
Country United Kingdom
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (5)
GSM1005488 NPCtotalRNA1
GSM1005489 NPCtotalRNA2
GSM1005490 ESCtotalRNA1
This SubSeries is part of SuperSeries:
GSE40896 Genome-wide nucleosome positioning during embryonic stem cell development
SRA SRP015796
BioProject PRJNA175502

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40948_MEF_vs_ESC_2replicates_expression.tsv.gz 10.8 Mb (ftp)(http) TSV
GSE40948_NPC_vs_ESC_2replicates_result_10.transcript_summary.tsv.gz 11.5 Mb (ftp)(http) TSV
GSE40948_RAW.tar 1.2 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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