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| Status |
Public on Dec 01, 2015 |
| Title |
e7.5 EPC Input (1) |
| Sample type |
SRA |
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| Source name |
Placenta
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| Organism |
Mus musculus |
| Characteristics |
strain: CD1
tissue: placenta
age: e7.5
chip antibody: none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Ectoplacental cone (EPC) tissue was dissected from embryos at e7.5 and e9.5, obtained from timed pregnant CD-1 mice (Charles Rivers Labs). The EPC was separated from the maternal decidua, embryo, and other extraembryonic tissue. Chromatin isolation and immunoprecipitation were carried out as previously described (Tuteja et al. 2008 Nucleic Acid Research 36(12): 4149-4157) but with 5μg chromatin and 1.2μg of H3k27ac antibody (Abcam ab4729, lot: GR24371-1) for the immunoprecipitation assay.
For each sample of immunoprecipitated DNA, 2ng were modified for sequencing following the Illumina's protocol (Preparing Sample for ChIP Sequencing of DNA (11257047 Rev A)).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Read alignment: Sequencing output was analyzed using the Illumina Genome Analyzer Pipeline. Sequence tags that aligned uniquely to the reference genome with zero, one, or two mismatches, according to the ELAND alignment algorithm, were used for further analysis.
Sequence tags from biological replicates were combined prior to peak calling. Peak calling was performed using GLITR (Tuteja et al. 2008 Nucleic Acid Research 36(12): 4149-4157) with default parameters, a 5% false discovery rate cutoff, and a maximum peak height ≥20. Data were further filtered to remove peaks that were also identified in input control data, and to remove peaks that overlapped exons (using the UCSC mm9.knownGene table) or that were within 2.5kb of a gene transcriptional start site.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files that have the coordinates of each called peak.
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| Submission date |
Feb 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Geetu Tuteja |
| Organization name |
Iowa State University
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| Department |
Genetics, Development and Cell Biology
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| Street address |
2106 Molecular Biology Building
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| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
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| Platform ID |
GPL11002 |
| Series (2) |
| GSE65807 |
Combining ChIP-Seq and RNA-Seq data in early placental development to study trophoblast invasion [ChIP-Seq] |
| GSE65809 |
Combining ChIP-Seq and RNA-Seq data in early placental development to study trophoblast invasion |
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| Relations |
| BioSample |
SAMN03339469 |
| SRA |
SRX871502 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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