|
| Status |
Public on Aug 10, 2016 |
| Title |
WT H2B IP - replicate 2 |
| Sample type |
genomic |
| |
|
| Source name |
Formaldehyde crosslinked and sonicated DNA from wild-type yeast
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
treatment: sonication + anti-H2B antiboty for ChIP
genotype: WT
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 Within 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 |
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