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Sample GSM2494918 Query DataSets for GSM2494918
Status Public on Dec 12, 2017
Title Mixed_Embryo_Input_ChIP-Seq
Sample type SRA
 
Source name Mixed preZGA and postZGA chromin
Organism Danio rerio
Characteristics developmental stage: Mixed preZGA and postZGA chromin
strain: Tu
injection: NA
mutation: Wild Type
Growth protocol Standard zebrafish growth conditions.
Extracted molecule genomic DNA
Extraction protocol Whole embryos were cross-linked with 2.2% formaldehyde, then nuclei were extracted as described in Potok et al. Cell 2013. Nuclei preps were then combined and sonicated using a Branson Sonicator. Antibodies were then added to each lysate to bind overnight. The following day protein A/G dynabeads were then used to precipitate antibody bound chromatin (bead binding was for 4 hours at 4C). Bead bound chromatin was then washed and eluted using standard ChIP techniques.
NEBNext ChIP-Seq Library Prep Reagents
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description Precipitated Genomic DNA from Chromatin
Processed data file: none
Data processing Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -r Random -k -Q 13 -o SAM
Sam files were then combined due to high correlation between technical and biological replicates.
Macs2 was then used to generate read count normalized genome wide pileup tracks and lambda tracks for precipitated samples and input. (callpeak --nomodel --extsize 150 --SPMR)
Pileup tracks were then Input corrected using the Macs2 subtract function (bdgcmp -m subtract).
Log10 Fold enrichment was then calculated for each sample comparing input corrected pileups to input lambda. (bdgcmp -m logFE).
Peaks were then called as regions with greater than 3 fold enrichment over lambda using the Macs2 bdgpeakcall function. (bdgpeakcall -c 0.477 -l 100 -g 100)
Genome_build: Zv10
Supplementary_files_format_and_content: bed and bigWig files
 
Submission date Feb 17, 2017
Last update date May 15, 2019
Contact name Patrick Murphy
Organization name Huntsman Cancer Institute
Street address 2000 Circle of Hope Way
City SLC
State/province UT
ZIP/Postal code 84112
Country USA
 
Platform ID GPL18413
Series (2)
GSE95030 ‘Placeholder’ nucleosomes underlie germline-to-embryo DNA methylation reprogramming [ChIP-Seq]
GSE95033 ‘Placeholder’ nucleosomes underlie germline-to-embryo DNA methylation reprogramming
Relations
BioSample SAMN06345544
SRA SRX2574256

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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