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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 27, 2018 |
| Title |
Input from HCT116 RepID KO cells |
| Sample type |
SRA |
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| Source name |
Colon carcinoma
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: Cultured cancer cell line
chip antibody: none
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| Growth protocol |
Cancer cells were grown in DMEM medium, 10% FBS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using each antibodies. Enriched DNA molecules were then amplified randam primer with klenow fragment and sequenced by Illumina Genome Analyzer IIx.
Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit).
Illumina paired-end sequencing
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
For RepID ChIP, the MACS peak calling program was used comparing reads from the ChIP –seq experiment to genomic input reads from the same cell line, with default parameters, and a p-value = 1e-9.
For nascent strand peak calling the SICER program was used. Nascent strand reads were called by comparison to HCT116 genomic reads using a window size of 200bp, gap size of 600pb, and FDR of 0.00001. For ChiP sequencing peak calling, the SICER program was used except for H4K16Ac ChIP, which are called peaks by broad MACS. For peak calling, used same length sequenced genomic control (101bp or 125bp)
Illumina single read 105bp or 125bp sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq
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| Submission date |
May 21, 2018 |
| Last update date |
Jun 27, 2018 |
| Contact name |
Christophe E Redon |
| E-mail(s) |
redonc@mail.nih.gov
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| Phone |
240-760-7338
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| Organization name |
NIH
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| Street address |
37 Convent Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE114703 |
The Replication-initiation determinant protein (RepID) modulates replication by recruiting CUL4 to chromatin |
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| Relations |
| BioSample |
SAMN09232391 |
| SRA |
SRX4107933 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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