|
Status |
Public on Mar 23, 2023 |
Title |
YZ6_ESR2SUZ12E3N, input |
Sample type |
SRA |
|
|
Source name |
Ishikawa
|
Organism |
Homo sapiens |
Characteristics |
cell line: endometrial adenocarcinoma fraction: input treatment: Treated with vecle vehicle control for 24 hours
|
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 23, 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 |
SAMN26903072 |
SRA |
SRX14592985 |