|
| Status |
Public on Jul 13, 2017 |
| Title |
GATA6_CHIP |
| Sample type |
SRA |
| |
|
| Source name |
hES-Derived Definitive Endoderm cells
|
| Organism |
Homo sapiens |
| Characteristics |
passage: Between 40-50
line: H1
pulldown method: Magnetic Streptavidin Beads
|
| Treatment protocol |
Cells were treated with 1ug/mL doxycycline for 24 hours prior to harvest
|
| Growth protocol |
H1 hESCs containing dox-inducible Avi-tagged hGATA6 and BirA transgenes were differentiated into definitive endoderm by treatment with Activin A (4 days), and BMP4 and bFGF (first two days) in RPMI 1640 medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked for 10 minutes with 1% formaldehyde, which was quenched with 125mM glycine. The cells were washed 3X with ice cold PBS+protease inhibitors+PMSF, and scraped into tubes. Chromatin was sheared in a Diagenode Bioruptor Pico to 150-600bp fragments. Input chromatin was saved for "input sample" and the remainder of the chromatin was pulled down using streptavidin beads. Bound chromatin and input DNA samples had the crosslinks reversed, the DNA was purified by phenol/chloroform extraction and ethanol precipitation, and the purified DNA samples were submitted to Beijing Genomics Institute for Library Generating and Sequencing.
Library generated by Beijing Genomics Institute
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Samples were sequenced on Illumina HiSeq 2000
Alignment to the Human genome build hg19 was performed using Bowtie2 with option -k 1
Peak calling was done using MACS2 2.1.0 with FDR 0.05
Genome_build: hg19
Supplementary_files_format_and_content: bdg files were generated using MACS2
|
| |
|
| Submission date |
Jan 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen A Duncan |
| E-mail(s) |
duncanst@musc.edu
|
| Phone |
843-792-9104
|
| Organization name |
Medical University South Carolina
|
| Department |
Regenerative Medicine and Cell Biology
|
| Lab |
Duncan Lab
|
| Street address |
173 Ashley Avenue, BSB 6th Floor, Room 657A
|
| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
29425 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE77360 |
Gene Expression Changes in Definitive Endoderm in response to GATA6-depletion (ChIP-seq) |
| GSE81901 |
Gene Expression Changes in Definitive Endoderm in response to GATA6-depletion |
|
| Relations |
| BioSample |
SAMN05177258 |
| SRA |
SRX1799987 |
