|
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.
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|
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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
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|
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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 |