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Sample GSM6675614 Query DataSets for GSM6675614
Status Public on Oct 26, 2022
Title Delta82D26_Input
Sample type SRA
 
Source name Neurospora tissue
Organism Neurospora crassa
Characteristics tissue: Neurospora tissue
genotype: del.ncu09482
time: 26 hr
Treatment protocol shaking
Growth protocol 2% LCM medium, 25 degrees, in the dark for 20 hrs for WT while 26 hrs for the mutant
Extracted molecule genomic DNA
Extraction protocol Neurospora tissue was cross-linked with 3% formaldehyde for 15 min and quenched with 0.25 M glycine for 5 min. Tissue was then washed with PBS three times and vacuum-dried; 0.4 g was weighed, cut into 9 pieces, and each piece soaked in 0.5 ml SDS lysis buffer (50 mM Tris/HCL [pH 8.0], 1% SDS, 5 mM EDTA) containing Roche protease inhibitors (Sigma-Aldrich, Catalog # 11836170001). The soaked tissue was first sonicated for 8 sec for three times at 30% amplitude with a Bronson sonicator equipped with a microtip, and then further sonicated in a water bath sonicator 5 times for 5 min each with an interval of 30 sec on and 30 sec off.
The purified ChIP DNA was end-repaired and ligated to Ion-compatible barcode adapters using Ion XpressTM Plus Fragment kit (Catalog # 4471269) and Ion XpressTM Barcode Adapters (Catalog # 4471250). The final libraries were purified with two rounds of AMPure XP Bead capture to size select fragments between 160 to 340 bps in length. The emulsion clonal bead amplification to generate bead templates for the Ion Torrent platform was performed on the Ion Chef System (Thermo Fisher Scientific) with the Ion PI™ Hi-Q™ Chef Kit (Thermo Fisher Scientific, Catalog # A27198) and Ion PI™ Chip Kit v3 (Thermo Fisher Scientific, Catalog # A26771).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Ion Torrent PGM
 
Description Ion Chef System
Data processing Samples were mapped to the Neurospora crassa genome (from GenBank) using TMAP (Ion 569 Software, https://github.com/iontorrent/TMAP)
Peaks were called using MACS2 (https://github.com/taoliu/MACS).
Peaks were annotated with ChIPseeker (Bioconductor, https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html).
In addition to MACS2, the SICER software (https://home.gwu.edu/~wpeng/Software.htm) was used to identify peaks and identify differentially abundant peaks between WT and mutant strains.
For comparison of WT vs. control in histone and acetylated histone, three runs apiece were performed with window sizes of 200, 400 and 600, and gap sizes of 600, 1,200 and 1,800, respectively.
Redundant peaks between the three runs (within 2,500 bp) were eliminated with a simple R script. Another script was used to identify genes within 1,000 bp from either border of the peaks.
Assembly: NC12
Supplementary files format and content: bedgraph
 
Submission date Oct 25, 2022
Last update date Oct 26, 2022
Contact name Bin Wang
E-mail(s) bin.wang@dartmouth.edu
Phone 6036465276
Organization name Geisel School at Dartmouth
Department MSB
Street address Vail Loading Dock, Attn: 702 Remsen
City Hanover
State/province New Hampshire
ZIP/Postal code 03755
Country USA
 
Platform ID GPL32780
Series (1)
GSE216517 ChIP-seq H4 and AcH4 in WT and del.ncu09482
Relations
SRA SRX15127215
BioSample SAMN28058086

Supplementary file Size Download File type/resource
GSM6675614_mut_control_lambda.bedGraph.gz 17.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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