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Series GSE39406 Query DataSets for GSE39406
Status Public on Nov 21, 2012
Title Site-specific silencing of regulatory elements as a mechanism of X-inactivation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The inactive X chromosome’s (Xi) physical territory is microscopically devoid of transcriptional hallmarks and enriched in silencing-associated modifications. How these microscopic signatures relate to specific Xi sequence is unknown. This study reports the profiling of Xi gene expression and chromatin states at high-resolution via allele-specific sequencing in F1 hybrid mouse trophoblast stem cells (TSCs). Datasets provided include those generated from strand-specific RNA-Seq, ChIP-Seq, FAIRE-Seq, and DNase-Seq protocols. Included for each dataset are FASTQ files, BED alignments and WIG files with coordinates relative to UCSC genome build mm9, and _snp files that report the location of all SNP-overlapping reads.
Overall design The F1 TSC lines profiled were generated from crosses between CAST/EiJ (Cast) and C57BL/6J (B6) mice. C/B denotes a Cast mother and B6 father, and B/C denotes a B6 mother and Cast father.
Contributor(s) Calabrese JM
Citation(s) 23178118
Submission date Jul 16, 2012
Last update date May 15, 2019
Contact name J Mauro Calabrese
Phone 919-843-3257
Organization name UNC-Chapel Hill
Department Pharmacology
Street address 120 Mason Farm Road
City Chapel Hill
State/province NC
ZIP/Postal code 27516
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (17)
GSM967642 C/B RNA
GSM967643 B/C RNA
GSM967644 Pol II
BioProject PRJNA170844
SRA SRP014437

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
GSE39406_RAW.tar 14.2 Gb (http)(custom) TAR (of BED, TXT, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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