|
| Status |
Public on May 08, 2019 |
| Title |
E2-1h.HiC |
| Sample type |
SRA |
| |
|
| Source name |
uterus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: uterus
strain: C57BL/6J
|
| 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 |
HiC: Illumina-compatible sequencing libraries were prepared by first shearing purified Arima-HiC proximally-ligated DNA and then size-selecting DNA fragments from ~200-600bp using solid phase reversible immobilization (SPRI) magnetic beads. The size-selected fragments were then enriched for biotin and converted into Illumina-compatible sequencing libraries using the KAPA Biosystems Hyper Prep kit (Wilmington, MA). After adapter ligation, DNA was PCR amplified and purified using SPRI beads.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The HiC reads were processed with the Juicer platform (v1.5.6) to generate contact matrix files in ~.hic format and to identify chromatin loops.
genome build: mm10
processed data files format and content: HiC contact matrix in ~.hic format
processed data files format and content: HiC loops in tab-delimited text format
|
| |
|
| Submission date |
Jan 31, 2019 |
| Last update date |
May 13, 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 |
GPL24247 |
| Series (1) |
| GSE125972 |
A distal super enhancer mediates estrogen-dependent mouse uterine–specific gene transcription of Insulin-like growth factor 1 (Igf1) |
|
| Relations |
| BioSample |
SAMN10854703 |
| SRA |
SRX5318307 |
