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Status |
Public on Nov 30, 2016 |
Title |
Wnt3a 6h RNA-seq |
Sample type |
SRA |
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Source name |
H1-hESC
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Organism |
Homo sapiens |
Characteristics |
treatment: Wnt3a 6h
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Treatment protocol |
H1 cells treated with 25ng/ml Activin A, 25ng/ml Wnt3a and both of them for 6h or 24h in B27-Chemical defined medium for 6h and 24h
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Growth protocol |
H1 cells cultured in N2B27-Chemical defined meiudm on matrigel
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Extracted molecule |
total RNA |
Extraction protocol |
H1 cells were lysised with TriZol regent to get RNA libraries were set up by Berry Genomics BeiJing
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
polyA mRNA
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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
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Organization name |
NHLBI
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Department |
System Biology Center
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Lab |
Laboratory of Epigenome Biology
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Street address |
9000 Rockville Pike
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City |
Bethesda |
State/province |
Maryland |
ZIP/Postal code |
20892 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE81617 |
Activin/Smad2-induced H3K27me3 reduction is crucial to initiate mesendoderm differentiation of ES Cells |
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Relations |
BioSample |
SAMN05013694 |
SRA |
SRX1774222 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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