|
Status |
Public on Nov 30, 2016 |
Title |
Control H3K27me3 ChIP-seq |
Sample type |
SRA |
|
|
Source name |
H1-hESC
|
Organism |
Homo sapiens |
Characteristics |
treatment: None antibody: H3K27me3
|
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.
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|
|
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 |
SAMN05013699 |
SRA |
SRX1774227 |