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Sample GSM2138567 Query DataSets for GSM2138567
Status Public on Aug 10, 2016
Title HBR∆ H2B IP - replicate 1
Sample type genomic
 
Source name Formaldehyde crosslinked and sonicated DNA from HBR∆ (htb1-∆30-37) mutant yeast
Organism Saccharomyces cerevisiae
Characteristics treatment: sonication + anti-H2B antiboty for ChIP
genotype: htb1-∆30-37
antibody: anti-H2B
Treatment protocol Yeast cell cultures were cross-linked with 1% formaldehyde at room temperature for 15-20 minutes, and then the cells were pelleted and snap-frozen in liquid nitrogen.
Growth protocol Yeast cultures (60 ml) were grown in YPD medium to mid-log phase
Extracted molecule genomic DNA
Extraction protocol Yeast cells were lysed with glass beads in a multi-tube vortexer for 2 hours at 4˚C . The extracts were sonicated, yielding DNA fragments ~400 bp in size on average. ChIP was performed using an anti-histone H2B polyclonal antibody.
Label biotin
Label protocol IP and Input samples were end-repaired using T4 DNA polymerase, ligated to adaptors, and PCR amplifed (Ligation Mediated-PCR). The resulting PCR products were fragmented and labeled using the GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix), according to the the manufacturer’s instructions.
 
Hybridization protocol Samples were hybridized to Affymetrix S. cerevisiae Tiling 1.0R arrays according to Affymetrix specifications.
Scan protocol Samples were scanned on Affymetrix S. cerevisiae Tiling 1.0R arrays according to Affymetrix specifications.
Description Quantile Normalized Between Groups (TAS software)
Data processing Signal intensity data was analyzed using Affymetrix Tiling Analysis Software (TAS, version 1.1), using default settings, except for a bandwidth of 60 and target intensities were scaled to 500. Normalization is described in the Description column under Samples.
Wig files were generated using a custom Perl script to convert the text output to a wig output. Note, data is Log2(IP/input)
 
Submission date Apr 29, 2016
Last update date Aug 10, 2016
Contact name John J. Wyrick
E-mail(s) jwyrick@vetmed.wsu.edu
Phone 509-335-8785
Organization name Washington State University
Department School of Molecular Biosciences
Street address Biotechnology Life Sciences 241
City Pullman
State/province WA
ZIP/Postal code 99164
Country USA
 
Platform ID GPL7250
Series (1)
GSE80831 A Basic Domain in the Histone H2B N-terminal Tail is Important for Nucleosome Assembly by FACT

Supplementary file Size Download File type/resource
GSM2138567_HBR_H2B_IP1_vs_HBR_Input_scale500_bandwidth60_4_6.wig.gz 13.1 Mb (ftp)(http) WIG
GSM2138567_Kryss-4-031810.CEL.gz 25.7 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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