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Sample GSM3587126 Query DataSets for GSM3587126
Status Public on May 08, 2019
Title 21d_E2-1h.H3K27ac_ChIPseq
Sample type SRA
 
Source name uterus
Organism Mus musculus
Characteristics tissue: uterus
strain: C57BL/6J
antibody: Active Motif #39133
Treatment protocol Mice were either used at 21 days old or were ovariectomized at 10 weeks old, held for 10-14 days to allow endogenous hormones to clear. Mice were given a single intraperitoneal injection of 250 ng E2 dissolved in 0.1 ml of normal saline or 1 mg P4 dissolved in sesame oil. Control vehicle (V) animals were injected with 0.1 ml normal saline. Tissue samples were collected 1, 2, 6, 8 12 or 24 hours after the injections.
Extracted molecule genomic DNA
Extraction protocol ChIP-seq: Frozen mouse tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp.
ChIP-seq: Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing ChIP-seq reads were filtered to retain only read pairs with mean base quality score >20. ERa ChIP-seq samples were hard-clipped to 36nt. SMC1a ChIP-seq samples were submitted to cutadapt v1.2.1 with parameters "-a AGATCGGAAGAG -O 5 q 0" to trim adapter, then filtered to retain only reads at least 30nt in length.
Trimmed & filtered ChIP-seq reads were mapped to mm10 via Bowtie allowing only uniquely-mapped hits (parameter "-m 1"), then coordinate-sorted and deduplicated via the Picard tool suite.
Normalized depth tracks for ChIP-seq data were generated by BEDTools genomeCoverageBed after extending all uniquely-mapped non-duplicate reads to average fragment size (150nt for ERa, 200nt for all others), then normalized to 15M (for ERa) or 20M (all others) and converted to bigWig format with UCSC utility bedGraphToBigWig.
genome build: mm10
processed data files format and content: ChIP-seq and RNA-seq normalized depth track in bigWig format
 
Submission date Jan 31, 2019
Last update date May 11, 2019
Contact name Sylvia C Hewitt
E-mail(s) sylvia.hewitt@nih.gov, curtiss@niehs.nih.gov
Phone 9842874317
Organization name NIEHS
Department RDBL
Lab Pregnancy & Female Reproduction
Street address 111 Alexander Dr
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL19057
Series (1)
GSE125972 A distal super enhancer mediates estrogen-dependent mouse uterine–specific gene transcription of Insulin-like growth factor 1 (Igf1)
Relations
BioSample SAMN10854685
SRA SRX5318287

Supplementary file Size Download File type/resource
GSM3587126_21d_E2-1h.H3K27ac_ChIPseq.normDepth.bigWig 228.8 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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