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Sample GSM1701828 Query DataSets for GSM1701828
Status Public on Feb 02, 2016
Title hNPC SOX2 ChIP-seq
Sample type SRA
Source name H9 derived NPCs
Organism Homo sapiens
Characteristics cell type: hESC
chip antibody: SOX2 (R&D 2018)
Growth protocol H9 cells were maintained in mTeSR1 in BD hESC qualified matrigel coated dishes. Culture was daily changed, and hESCs were passaged using Accutase or 1mg/ml dispase. hNPCs were differentiated from H9 cells using established protocol (Chambers SM, Nat Biotechnol, 2009; 27: 275–280). Briefly, we used Noggin (500ng/ml), SB431542 (10mM) and Compound C (10mM) to induce neural differentiaiton.Neural rosettes were picked up and replated onto matrigel coated dishes, and then dissociated into single NPCs and maintained in N2B27 medium supplemented with 10ng/ml bFGF. hNPCs were then passaged using 0.05% trypsin.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and SOX2-DNA complexes and POI II-DNA complexes were immunoprecipitated with SOX2 antibody (R&D AF2018) or POI II antibody (Covance MMS-126R). Protein A and G Magenetic Dynabeads were used to capture antibody bound protein-DNA complexes.
ChIP-seq libraries preparation: The ChIP-enriched DNA samples were treated with end-repair of the DNA, adding ‘‘A” bases to the DNA, ligating sequencing adapters to DNA fragments, amplifying adapter-modified DNA by PCR and gel purification for ChIPseq using NEBNext Ultra DNA Library Prep Kit for Illumina. Purified libraries were sequenced on Illumina HiSeq2500 platforms.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Data processing CASAVA1.8.2 convert per-cycle *.bcl files into FASTQ files
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7
peaks were called using MACS version 2.0.10 with the following setting: shift-size (73), q-value (0.01)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by MACS2, the score represents number of bp fall into the single base pair region.
Submission date Jun 02, 2015
Last update date May 15, 2019
Contact name Ying Jin
Organization name Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Street address 225 South Chongqing Road
City Shanghai
ZIP/Postal code 200025
Country China
Platform ID GPL16791
Series (1)
GSE69479 Genome-wide map of SOX2 occupancy in human ES cells (hESCs) and hESC derived neural progenitor cells (hNPCs)
BioSample SAMN03759641
SRA SRX1047416

Supplementary file Size Download File type/resource
GSM1701828_NPC_SOX2.bed.gz 535.1 Kb (ftp)(http) BED 282.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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