NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2159749 Query DataSets for GSM2159749
Status Public on Nov 30, 2016
Title Control H3K4me3 ChIP-seq
Sample type SRA
 
Source name H1-hESC
Organism Homo sapiens
Characteristics treatment: None
antibody: H3K4me3
Treatment protocol And treated with 25ng/ml Activin A, 25ng/ml Wnt3a and both of them for 2h and 6h in B27-Chemical defined medium for H3K27me3, H3K4me3 ChIP-seq.
Growth protocol H1 cells cultured in N2B27-Chemical defined meiudm on matrigel
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27me3 and H3K4me3 antibody.
libraries were set up by Berry Genomics BeiJing
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description ChIP DNA
Data processing For RNA-seq, paired-end reads were first trimmed the first 15 bps for each end and then mapped to human genome (hg19) using STAR (v2.4.0d), with the following options: --outFilterMultimapNmax 1, --outFilterMismatchNmax 7, --outFilterMismatchNoverLmax0.1, --outFilterMatchNminOverLread 0.4, --alignEndsType EndToEnd. Gene expression was estimated and normalized with Cuffnorm from the Cufflinks package (v2.2.1) into FPKM matrix using default parameters for the annotations GTF file downloaded from GENCODE (v19).
For ChIP-seq, reads were mapped into human genome (hg19) using bowtie (v1.1.0) with the options: -y –k 1 -m 1 –-best –-chunkmbs 200. MACS (v2.1.0) was used to identity significant binding events for each ChIP-seq data with options: -nomodel -extsize 75 - keep-dup 1 -broad. The bigWig profile fies wre generated by MACS with the setting -B --SPMR -g hs --nomodel --extsize 75 --fix-bimodal.
Genome_build: hg19
Supplementary_files_format_and_content: The bigWig profile fies were generated by MACS with the setting -B --SPMR -g hs --nomodel --extsize 75 --fix-bimodal. The gene.attr_table.txt and genes.fpkm_table.txt were generated by Cuffnorm using the GENCODE (v19) annotations.
 
Submission date May 18, 2016
Last update date May 15, 2019
Contact name Yaqiang Cao
E-mail(s) caoyaqiang0410@gmail.com
Organization name NHLBI
Department System Biology Center
Lab Laboratory of Epigenome Biology
Street address 9000 Rockville Pike
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platform ID GPL11154
Series (1)
GSE81617 Activin/Smad2-induced H3K27me3 reduction is crucial to initiate mesendoderm differentiation of ES Cells
Relations
BioSample SAMN05013700
SRA SRX1774228

Supplementary file Size Download File type/resource
GSM2159749_C_H3K4me3.bw 72.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap