GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM520621 Query DataSets for GSM520621
Status Public on Feb 25, 2011
Title H3K4me3_ChIPSeq
Sample type SRA
Source name whole embryo at 24 hours post fertilization, H3K4me3 ChIP
Organism Danio rerio
Characteristics tissue: whole embryo
developmental stage: 24 hours post fertilization
genotype: wild type
antibody: anti-H3K4me3
Growth protocol Wild type zebrafish embryos at 24 hours post fertilization.
Extracted molecule genomic DNA
Extraction protocol Histone-DNA complexes were isolated from sonicated chromatin using antibodies against H3K4me1 or H3K4me3. DNA was isolated and ends were polished using the END-IT DNA Repair Kit (Epicentre). Blunt ends were treated with exo-minus Klenow and dATP to add a protruding 3' adenosine. Standard Illumina adaptors were ligated and the resulting library was PCR amplified with Illumina primers for 15 cycles followed by gel purification of approximately 250 bp library fragments. Cluster generation and subsequent sequencing was performed on a Genome Analyzer according to manufacturer's specifications.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description Chromatin IP against H3K4me3
Data processing Alignments: Sequence reads were obtained and mapped to the zebrafish (Zv7) genome using the Illumina Genome Analyzer Pipeline. All reads uniquely mapped with two or fewer mismatches were retained for subsequent peak detection. The alignment files are in bed format.

Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS 1.3.6) algorithm ( with default setting except for these parameters --shiftsize=150 --oldfdr --gsize=1700000000 --tsize=36 --bw=150 --mfold=10. The peak files are in wig format.
Submission date Mar 10, 2010
Last update date May 15, 2019
Contact name Lihua Julie Zhu
Organization name Umass Medial School
Department Program in Gene Function and Expression
Street address 364 Plantation St
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
Platform ID GPL10164
Series (1)
GSE20600 Genome-wide identification of putative cis-regulatory elements through epigenetic profiling in zebrafish
SRA SRX018126
BioSample SAMN00010383

Supplementary file Size Download File type/resource
GSM520621_WT24hrMe3_6lanes_all.bed.gz 71.5 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA
Processed data are available on Series record

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