|
| Status |
Public on Jul 15, 2019 |
| Title |
TSC Input control |
| Sample type |
SRA |
| |
|
| Source name |
TS_input
|
| Organism |
Mus musculus |
| Characteristics |
cell line: F4
cell type: Trophoblast stem cells (TSCs)
chip antibody: None
|
| Treatment protocol |
trophoblast stem cells were fixed with formaldehyde, lysed and then sonicated with a Misonix Sonicator 3000.
|
| Growth protocol |
TS cells were maintained in RPMI1640 (Sigma) supplemented with 20% FBS (Life Technologies), 1mM sodium pyruvate (Life Technologies), 50U/ml penicillin, 50μg/ml streptomycin, 100mM 2-mercaptoethanol (Sigma), 2mM Glutamax (Life Technologies), 25ng/ml FGF4 (R & D Systems), and 1μg/ml heparin (Sigma), with 70% of the media preconditioned by mitotically inactivated E12.5 embryonic fibroblasts (70CM + F4H medium)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The lysate is incubated with 15ug anti-Esrrb antibody, ), washed, and the bound chromatin eluted. The eluate was reverse-crosslinked, and treated with proteinase K
The ChIP-enriched and corresponding input genomic DNA libraries were prepared using the Illumina Genomic Sample Preparation Kit (Illumina) according to the manufacturer’s instruction
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
FASTQ sequences were aligned to the mm9 genome using Bowtie2 v.2.2.3
Peak-calling was performed on the ChIP-Seq library using MACS v.2.2.1, using the following parameters (-g mm -q 0.01)
Genome_build: mm9
Supplementary_files_format_and_content: NarrowPeak (BED) file generated by MACS peakcalling
|
| |
|
| Submission date |
Dec 05, 2018 |
| Last update date |
Jul 15, 2019 |
| Contact name |
Eiichi Okamura |
| E-mail(s) |
eiokamu@gmail.com
|
| Organization name |
Shiga University of Medical Science
|
| Department |
Research Center for Animal Life Science
|
| Lab |
Department of Stem Cells and Human Disease Models
|
| Street address |
Seta, Tsukinowa-cho
|
| City |
Otsu |
| State/province |
Shiga |
| ZIP/Postal code |
520-2192 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE123361 |
Esrrb function in the extraembryonic ectoderm is required for proper primordial germ cell specification [ChIP-seq] |
| GSE123363 |
Esrrb function is required for proper primordial germ cell development in presomite stage mouse embryos |
|
| Relations |
| BioSample |
SAMN10523697 |
| SRA |
SRX5097635 |
