|
| Status |
Public on Oct 18, 2017 |
| Title |
GATA3 ChIP, biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
trophoblast progenitors at day 3_GATA3 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
source cell type: Human embryonic stem cells (hESC)
treated with: BMP4 for 3 day
cell type: trophoblast progenitors at day 3
chip antibody: anti-GATA3 (#CM405A, Biocare Medical)
|
| Treatment protocol |
For trophoblast differentiation, cells were seeded at 100% confluency on Matrigel-coated plates containing KSR-based differentiation medium and 50 ng/ml BMP4. During the time course, medium was changed every 24 hours.
|
| Growth protocol |
H9 cell line was grown on Geltrex-coated plates in mTESR1 medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP'ed DNA fragments were prepared using High Sensitivity ChIP kit (Active Motif, #53040) according to manufacturer's instrcutions using aforementioned antibodies
Libraries were prepared using NEBNext® ChIP-Seq Library Prep kit for Illumina (New England Biolabs, #E6200) according to manufacturer's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
GATA3_7
|
| Data processing |
FASTQ files were aligned to hg19(UCSC) using bowtie (default parameters but -m 1).
Calculation of genomic coverage vectors was performed for each sample after 200 bp read extension.
Coverages were exported in BEDGRAPH format.
Genome_build: hg19
Supplementary_files_format_and_content: BEDGRAPH
|
| |
|
| Submission date |
Oct 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Dmitry Shaposhnikov |
| E-mail(s) |
dmitry.shaposhnikov@helmholtz-muenchen.de
|
| Organization name |
Helmholtz Center Munich
|
| Street address |
Ingolstädter Landstraße 1
|
| City |
Neuherberg |
| ZIP/Postal code |
85764 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE105081 |
Genome wide mapping of chromatin binding sites of GATA2, GATA3, TFAP2A, TFAP2C transcription factors in trophoblast progenitors derived from human embryonic stem cells |
|
| Relations |
| BioSample |
SAMN07795612 |
| SRA |
SRX3292068 |
