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| Status |
Public on Jun 01, 2017 |
| Title |
R48-L3-Input-Sequences |
| Sample type |
SRA |
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| Source name |
Human corneal epithelial cells (HCE)
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Human corneal epithelial cells (HCE)
sample type: Input
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| Treatment protocol |
Cells were fixed and collected at approximately 50% confluence
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| Growth protocol |
HCE cells were grown in OccuLife medium (LifeLine Cell Technology) at 37C, 5%CO2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the Grhl3 antibody.
Sequencing libraries were generated for the H3K4me1, H3K4me3, H3K27ac, and Input samples using the NEB Next reagents and Illumina adaptors and oligos, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library (Schmidt, 2009). Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer.
Libraries were sequenced on the Illumina Hi-Seq 2000, with 50bp single end sequencing
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 1
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| Data processing |
Base-calls were made using RTA version 1.12.4.2
Reads were aligned to human genome hg19 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1)
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using SICER (v1.1), with input aligned sequences as the control file, and FDR <.05
Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: Human hg19
Supplementary_files_format_and_content: interval files from galaxy, containing chromosome and coordinates of peak locations (column headers; chromosome, start, stop, ChIP read count, Control read count, p value, fold change, and FDR threshold)
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| Submission date |
Jan 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Bogi Andersen |
| Organization name |
University of California, Irvine
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| Department |
Medicine
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| Lab |
Andersen
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| Street address |
839 Health Sciences Dr.
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| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE43499 |
Genome-wide analysis of histone modifications H3K4me3, H3K4me1, and H3K27ac in primary human corneal epithelial cells |
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| Relations |
| SRA |
SRX217067 |
| BioSample |
SAMN01886596 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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