|
| Status |
Public on Jan 25, 2017 |
| Title |
GATA2 Run 1 and 2 |
| Sample type |
SRA |
| |
|
| Source name |
Gata2
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse trophoblast stem cells
antibody: anti-GATA2
|
| Growth protocol |
Mouse TS cells were routinely cultured under stem condition utilising standard protocol consists of MEF conditioned media in the presence of FGF4 & heparin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were trypsinized and washed with PBS before fixing them with 1% paraformaldehyde. Fixed cells were used to prepare genomic DNA fargments using a sonicator. Sonicated fragments were immunoprecipitated using either anti-GATA2 or anti-GATA3 antibodies or non-specific IgG. Samples from three independent experiments were poooled and genomic libraries were sequenced in Illumina Genome Analyzer II and in Illumina HiSeq platforms to generate 35 bp single end reads.
Libraries were prepared by Illumina. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA 1.7, ChIP-seq reads were aligned to the mm9 genome assembly using ELANDv2 with default parameters. Two technical replicates of each sample were pooled, because each sample was sequenced twice due to insufficient read depth obtained in the first sequencing run. Peaks were called relative to IgG as a control. Coverages estimates were generated using MACS 1.4 with p value cuff off set at 1e-5. Peaks in bed files and coverage in wig files are converted to bigbed and bigwig using bedToBigBed and wigToBigWig respectively.
Genome_build: mm9
Supplementary_files_format_and_content: Bigbed for peaks, bigwig for coverage
|
| |
|
| Submission date |
Dec 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sumedha S Gunewardena |
| Phone |
9139456878
|
| Organization name |
University of kansas medical center
|
| Department |
Dept. of Molecular and Integrative Physiology
|
| Street address |
2146 West 39th Avenue
|
| City |
Kansas City |
| State/province |
Kansas |
| ZIP/Postal code |
66160 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE92287 |
Genetic Redundancy of GATA Factors in Extraembryonic Trophoblast Lineage Ensures Progression of both Pre and Postimplantation Mammalian Development [ChIP-seq] |
| GSE92295 |
Genetic Redundancy of GATA Factors in Extraembryonic Trophoblast Lineage Ensures Progression of both Pre and Postimplantation Mammalian Development |
|
| Relations |
| BioSample |
SAMN06133238 |
| SRA |
SRX2416653 |
