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Sample GSM2242765 Query DataSets for GSM2242765
Status Public on Jun 11, 2017
Title Mixl1_Input
Sample type SRA
 
Source name whole zebrafish embryos
Organism Danio rerio
Characteristics strain: AB
Stage: 30-50% epiboly
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 and heat-shocket for one hour at 37 degrees celcius prior to fixation
Extracted molecule genomic DNA
Extraction protocol Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification 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 TruSeq DNA Sample Prep Kit (Part# FC-121-2001) with the exception that Illumina adapters were diluted 1:100 prior to use.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1000
 
Data processing Reads were mapped to the Zv9 version of the genome with Bowtie using the following parameters: -y -m2 -k2 --best.
Peaks were called for each Mixl1 ChIP sample relative to this input sample using MACS with the following parameters: --gsize 1.3e+9 and –mfold 10 -pval 1e-5
Peak coordinates common to both ChIP replicates were identified for further analysis using custom Perl scripts
Genome_build: Zv9
Supplementary_files_format_and_content: Wig files for track visualization of ChIP and input data.
 
Submission date Jul 20, 2016
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 GPL16509
Series (2)
GSE84612 Genome-wide profiling of Ta, Tbx16 and Mixl1 binding in early zebrafish embryos
GSE84619 Microarray and ChIP-seq identification of Ta and Tbx16 target genes in zebrafish gastrulas and Mixl1 targets in blastulas
Relations
BioSample SAMN05420281
SRA SRX1961790

Supplementary file Size Download File type/resource
GSM2242765_Mixl1-input.wig.gz 193.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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