|
| Status |
Public on Mar 03, 2015 |
| Title |
H3K4me3 case1 w/ EP |
| Sample type |
SRA |
| |
|
| Source name |
Human endometrial stromal cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Endometrial stromal cells
condition: induction with estradiol (10-8 M) and medroxyprogesterone acetate (10-6 M)
chip antibody: H3K4me3 (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan).
|
| Treatment protocol |
To induce decidualization, ESC were incubated with or without E (10-8 mol/l) and MPA (10-6 mol/l) for 14 days.
|
| Growth protocol |
Human primary endometrial stromal cells (ESC) were isolated by the enzymatic digestion of minced endometrial tissues with collagenase followed by the separation using a 70 µm nylon mesh filter. ESC were seeded at 105 cells/cm2 in 75 cm2 tissue culture flasks and incubated in Phenol Red-free DMEM containing glutamine, antibiotics, and dextran-coated charcoal-stripped FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonication/enzymatic digested nuclei and histone-DNA complexes were isolated with antibody.
The ChIP DNA and the Input DNA ends were repaired using T4 DNA polymerase, Klenow enzyme, and T4 polynucleotide kinase(PNK) (New England Biolabs), followed by treatment with Klenow exo- to add an A base to the 3’ end. After ligation of the Solexa adaptor using TaKaRa ligation Mix (TaKaRa), the adaptor-ligated DNAs were amplified using Solexa PCR primers for 18 cycles, and the amplified library was isolated from an agarose gel. The samples were purified using the QIAquick MinElute kit (Qiagen) at each preparation step. The purified library was used for cluster generation and sequencing analysis using the Genome Analyzer GAIIx (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 1.0.0 with the default parameters
Identification of differentially modified regions:
To examine whether histone modification statuses are altered throughout the genome during decidualization in ESC, histone modification signlas were searched in 1-kb intervals between -10 kb from transcription start site and +10 kb from transcription termination site. Then the difference in the signals between control ESC and decidualized ESC was evaluated by log2-transformed FPKM values. We defined the regions with more than 2-fold changes in the FPKM values as the differentially modified regions.
Genome_build: hg19
Supplementary_files_format_and_content: .bedgraph files; peak files in BED format
|
| |
|
| Submission date |
Apr 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Isao Tamura |
| E-mail(s) |
[email protected]
|
| Phone |
+81 836 22 2289
|
| Organization name |
Yamaguchi University Graduate School of Medicine
|
| Department |
Department of Obstetrics and Gynecology
|
| Street address |
Minami-Kogushi 1-1-1
|
| City |
Ube |
| ZIP/Postal code |
755-8505 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE57007 |
Genome-wide analysis of histone modifications in human endometrial stromal cells [ChIP-Seq] |
| GSE57010 |
Genome-wide analysis of histone modifications in human endometrial stromal cells |
|
| Relations |
| BioSample |
SAMN02732306 |
| SRA |
SRX524962 |
