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Sample GSM3139251 Query DataSets for GSM3139251
Status Public on Jul 17, 2018
Title input.s1
Sample type SRA
 
Source name hES-RPE
Organism Homo sapiens
Characteristics cell type: ES-derived RPE cells
chip antibody: none
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.
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description Sox9_merge_peaks.bed
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
 
Submission date May 10, 2018
Last update date Jul 17, 2018
Contact name Ran Elkon
Organization name Tel Aviv University
Department Human Genetics
Street address Ramat Aviv
City Tel Aviv
ZIP/Postal code 69494
Country Israel
 
Platform ID GPL16791
Series (1)
GSE114305 ChIP-seq analysis of SOX9 in hES-RPE cells
Relations
BioSample SAMN09112318
SRA SRX4065341

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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