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Sample GSM1254752 Query DataSets for GSM1254752
Status Public on Oct 15, 2014
Title Eomesa_ChIP1
Sample type SRA
 
Source name high-sphere stage embryos
Organism Danio rerio
Characteristics strain: AB
developmental stage: high-sphere
chip antibody: Eomesa
Treatment protocol Embryos fixed in 1.85% formaldehyde for 15 mins prior to chromatin extraction
Growth protocol Embryos grown in E3 embryo medium at 28.5 degrees celcius
Extracted molecule genomic DNA
Extraction protocol Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification from was used to obtain chromatin of appropriate fragment size. Desired protein-DNA complexes were isolated using antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Data processing Sequence reads were aligned to the Zv9 mouse genome release using Bowtie with the following options: -n2 –e120 –l 28 -m2 -k2 -best
Peaks were called in ChIP samples over input using MACS with the following options: −−mfold8 –pvalue 1e-4
Peak coordinates common to both ChIP replicates were identified for further analysis using custom Perl scripts
Genome_build: Zv9
Supplementary_files_format_and_content: peak wig files were generated using MACS. Peak bed files were generated using MACS followed by custom Perl scripts.
 
Submission date Oct 30, 2013
Last update date May 15, 2019
Contact name Andrew Christopher Nelson
E-mail(s) a.nelson.1@warwick.ac.uk
Organization name University of Warwick
Department School of Life Sciences
Street address Gibbet Hill Campus
City Coventry
ZIP/Postal code CV4 7AL
Country United Kingdom
 
Platform ID GPL9319
Series (2)
GSE51891 Genome-wide profiling of Smad2 and Eomesa binding in zebrafish blastulas
GSE51894 Smad2 and Eomesa
Relations
BioSample SAMN02389005
SRA SRX370997

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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