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| Status |
Public on Jul 17, 2018 |
| Title |
input.s2 |
| Sample type |
SRA |
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| Source name |
hES-RPE
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| Organism |
Homo sapiens |
| Characteristics |
cell type: ES-derived RPE cells
chip antibody: none
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| Growth protocol |
For RPE differentiation, hESCs colonies (Hes1 hES) were picked up using collagenase IV (1 mg/ml; 200 U/mg, Gibco-BRL, Gaithersburg, MD), and cultured using differentiation protocol including treatment with nicotinamide and activinA. After 6-10 weeks in suspension, pigmented clusters were triturated, plated on gelatin (Sigma) coated plates (Corning Incorporated, Corning, NY), and cultured in Knock out medium with 10mM nicotinamide for 3-5 weeks. The RPE cell lines were further propagated using TrypLE Select (Gibco-BRL). The cells were passaged every 2 weeks.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sonicated chromatin from hES-RPE cells was immunoprecipitated with rabbit anti SOX9 ( Millipore, AB5535 ).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Prep Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sox9_merge_peaks.bed
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| Data processing |
Sequenced reads were aligned to the human genome (hg19) using Bowtie2
SOX9 peaks were detected using MACS2; 1146 peaks detected
Genome_build: hg19
Supplementary_files_format_and_content: processed file contains the genomic coordinates of the 1,146 peaks (bed format) and "fold_enrichment" info for the peaks
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| Submission date |
May 10, 2018 |
| Last update date |
Jul 17, 2018 |
| Contact name |
Ran Elkon |
| Organization name |
Tel Aviv University
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| Department |
Human Genetics
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| Street address |
Ramat Aviv
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| City |
Tel Aviv |
| ZIP/Postal code |
69494 |
| Country |
Israel |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE114305 |
ChIP-seq analysis of SOX9 in hES-RPE cells |
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| Relations |
| BioSample |
SAMN09112317 |
| SRA |
SRX4065342 |
| 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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