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Series GSE58101 Query DataSets for GSE58101
Status Public on Jul 08, 2014
Title High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Mammalian embryonic stem (ES) cells and sperm exhibit unusual chromatin packaging that plays important roles in cellular function. Here, we extend a recently developed technique, based on deep paired-end sequencing of lightly digested chromatin, to assess footprints of nucleosomes and other DNA-binding proteins genome-wide in murine ES cells and sperm. In ES cells, we recover well-characterized features of chromatin such as promoter nucleosome depletion, and further identify widespread footprints of sequence-specific DNA-binding proteins such as CTCF, which we validate in knockdown studies. We document global differences in nuclease accessibility between ES cells and sperm, finding that the majority of histone retention in sperm preferentially occurs in large gene-poor genomic regions, with only a small subset of nucleosomes being retained over promoters of developmental regulators. Finally, we describe evidence that CTCF remains associated with the genome in mature sperm, where it could play a role in organizing the sperm genome.
 
Overall design We use Micrococcal Nuclease (MNase) to map chromatin structure in mouse ES cells and sperm. Specifically, we generate paired-end deep-sequencing libraries that are able to distinguish DNA digestion products by size, thus allowing us to simultaneously map nucleosomes as well as other DNA-binding proteins such as transcription factors.
 
Contributor(s) Rando OJ, Carone BR, Hung JH
Citation(s) 24998598
Submission date May 29, 2014
Last update date May 15, 2019
Contact name Benjamin R Carone
E-mail ben.carone@gmail.com
Organization name UMass Medical School
Department BMP
Street address 364 Plantation St
City Worcester
State/province Massachusetts
ZIP/Postal code 01605
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (17)
GSM1400766 MNase ESC unspun
GSM1400767 MNase ESC spun
GSM1400768 MNase Sperm spun
Relations
BioProject PRJNA248901
SRA SRP042377

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
GSE58101_RAW.tar 1.7 Gb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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