|
Status |
Public on Dec 12, 2017 |
Title |
Sperm_H3K27ac_ChIP-Seq_Rep1 |
Sample type |
SRA |
|
|
Source name |
Sperm
|
Organism |
Danio rerio |
Characteristics |
developmental stage: Sperm 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: H3K27ac_Sperm_Log10FE_over_Input_Lambda.bw; H3K27ac_Sperm_Peaks_Log10FE_3fold.bed
|
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
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|
|
Submission date |
Feb 17, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Patrick Murphy |
Organization name |
University of Rochester
|
Street address |
601 Elmwood Ave
|
City |
Rochester |
State/province |
NY |
ZIP/Postal code |
14642 |
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 |
SAMN06345583 |
SRA |
SRX2574276 |