|
| Status |
Public on Mar 23, 2023 |
| Title |
YZ8_ESR2SUZ12E3Y |
| Sample type |
SRA |
| |
|
| Source name |
Ishikawa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: endometrial adenocarcinoma
fraction: ChIP
treatment: Treated with Estriol for 24 hours, first IP with ERS2 antibody, then for the second IP with SUZ12
|
| Treatment protocol |
Ishikawa cells (~70% confluence) were transfection with 40ug of either pcDNA 3.1(+)/Flag-ERα or pcDNA /Flag-ERβ for 18 hours and subsequently treated with E3 for another 24 hours .
|
| Growth protocol |
Ishikawa cells were maintained in MEM (Sigma-Aldrich, MO) both containing 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody.
Samples are sequenced using 100bp paired-end sequencing on an Illumina HiSeq 4000 according to Illumina protocols.Briefly, approximately 5-10ng of DNA is cleaned up using Ampure XP SPRI beads (Beckman Coulter Genomics). The DNA is then end-repaired, A-tailed, adapter ligated and PCR enriched (8 -10 cycles). Indexed libraries that meet appropriate cut-offs are quantified by both RT-qPCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX. Samples with a yield of ≥0.5 ng/µl are used for sequencing. Flow Cell Preparation and Sequencing: Sample concentrations are normalized to 1 nM and loaded onto an Illumina HiSeq4000 flow cell at a concentration that yields 25 - 50 million passing filter clusters per sample. Samples are sequenced using 100bp paired-end sequencing on an Illumina HiSeq 4000 according to Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Data generated during sequencing runs are simultaneously transferred to the YCGA high-performance computing cluster
Supplementary files format and content: bedGraph
|
| |
|
| Submission date |
Mar 24, 2022 |
| Last update date |
Mar 24, 2023 |
| Contact name |
Yuping Zhou |
| E-mail(s) |
joezhouyp@gmail.com
|
| Organization name |
Yale
|
| Department |
OB/GYN
|
| Lab |
Taylor Lab
|
| Street address |
310 cedar street
|
| City |
new haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE199214 |
The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract |
| GSE199293 |
The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN26903075 |
| SRA |
SRX14592982 |
