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Series GSE75480 Query DataSets for GSE75480
Status Public on Dec 01, 2016
Title Functional roles of Aves class specific cis-regulatory elements on macroevolution of bird-specific features
Organism Gallus gallus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We carried out a comparative genomic analysis of 48 avian species to identify avian-specific highly conserved elements (ASHCEs). We performed genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) for three enhancer-associated histone modifications (H3K4me1, H3K27ac, H3K27me3), to investigate dynamic regulatory roles of ASHCEs in chicken development. We found that all three enhancer-associated histone marks are enriched in ASHCEs compared to the whole genome background.
Overall design ChIP-seq analyses for three known enhancer-associated histone modifications (H3K4me1, H3K27ac and H3K27me3) with samples from developing chicken embryos at stages HH16, HH21 and HH32 respectively and samples from developing limbs at stages HH21 and HH32 respectively with two biological replicates.
Contributor(s) Li C, Seki R, Irie N, Tamura K, Zhang G
Citation(s) 28165450
Submission date Nov 30, 2015
Last update date May 15, 2019
Contact name CNSA CNGB
Organization name BGI
Street address BGI
City shenzhen
ZIP/Postal code 518083
Country China
Platforms (1)
GPL16133 Illumina HiSeq 2000 (Gallus gallus)
Samples (40)
GSM1956865 HH16_whole_H3K27ac_r1
GSM1956866 HH16_whole_H3K27ac_r2
GSM1956867 HH16_whole_H3K27me3_r1
BioProject PRJNA304426
SRA SRP066802

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE75480_HH16_whole_H3K27ac_overlaps.finalPeaks.txt.gz 832.1 Kb (ftp)(http) TXT
GSE75480_HH16_whole_H3K27me3_overlaps.finalPeaks.txt.gz 261.6 Kb (ftp)(http) TXT
GSE75480_HH16_whole_H3K4me1_overlaps.finalPeaks.txt.gz 1.0 Mb (ftp)(http) TXT
GSE75480_HH21_limb_H3K27ac_overlaps.finalPeaks.txt.gz 893.0 Kb (ftp)(http) TXT
GSE75480_HH21_limb_H3K27me3_overlaps.finalPeaks.txt.gz 336.4 Kb (ftp)(http) TXT
GSE75480_HH21_limb_H3K4me1_overlaps.finalPeaks.txt.gz 633.8 Kb (ftp)(http) TXT
GSE75480_HH21_whole_H3K27ac_overlaps.finalPeaks.txt.gz 747.0 Kb (ftp)(http) TXT
GSE75480_HH21_whole_H3K27me3_overlaps.finalPeaks.txt.gz 333.2 Kb (ftp)(http) TXT
GSE75480_HH21_whole_H3K4me1_overlaps.finalPeaks.txt.gz 1.3 Mb (ftp)(http) TXT
GSE75480_HH32_limb_H3K27ac_overlaps.finalPeaks.txt.gz 818.9 Kb (ftp)(http) TXT
GSE75480_HH32_limb_H3K27me3_overlaps.finalPeaks.txt.gz 539.7 Kb (ftp)(http) TXT
GSE75480_HH32_limb_H3K4me1_overlaps.finalPeaks.txt.gz 645.6 Kb (ftp)(http) TXT
GSE75480_HH32_whole_H3K27ac_overlaps.finalPeaks.txt.gz 656.9 Kb (ftp)(http) TXT
GSE75480_HH32_whole_H3K27me3_overlaps.finalPeaks.txt.gz 324.9 Kb (ftp)(http) TXT
GSE75480_HH32_whole_H3K4me1_overlaps.finalPeaks.txt.gz 724.9 Kb (ftp)(http) TXT
GSE75480_RAW.tar 27.7 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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