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Sample GSM3139253

Query DataSets for GSM3139253

Status

Public on Jul 17, 2018

Title

SOX9.IP.rep1.s1

Sample type

SRA

Source name

hES-RPE

Organism

Homo sapiens

Characteristics

cell type: ES-derived RPE cells
chip antibody: rabbit anti-Sox9 (Millipore, AB5535)

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