|
| Status |
Public on Oct 16, 2014 |
| Title |
WT unstressed rep1 Snf2 mnase |
| Sample type |
SRA |
| |
|
| Source name |
yeast
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: WT
tissue: WCE
|
| Treatment protocol |
To induce stress cells grown in YPD were shifted to YNB + 0.5% dextrose
|
| Growth protocol |
Cells were grown in YPD
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Yeast whole cell extract were sonicated DNA-protein complexes were isolated with antibody.
ChiP-seq, Mnase-seq libraries were prepared using KAPA High Throughput Library Preparation Kit, Roche
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Primary analysis off the HiSeq 2000 machine was done with Illumina RTA v1.18.61, HiSeq Control Software v2.2.38, CASAVA version 1.8.2
Chip-seq: Reads were aligned using bowtie2 (2.1.0) with -k 1 to the yeast genome sacCer2 from UCSC.
Chip-seq: BAM files were read into R (3.0.2) and analyzed using packages GenomicRanges (1.14.4), Rsamtools(1.14.2), rtracklayer(1.22.0).
Chip-seq: bigWig files were created in R by calculating RPM (normalized coverage based on total bowtie2 alignments) and coverages were mean-smoothed with 101-base windows.
Mnase-seq: Reads were aligned using bowtie2 (2.1.0) to the yeast genome sacCer2 from UCSC.
Mnase-seq: BAM files were read into R (3.0.2) and analyzed using packages GenomicRanges (1.14.4), Rsamtools(1.14.2), rtracklayer(1.22.0).
Mnase-seq: bigWig files were created in R by calculating the midpoint of each fragment alignment (for fragments between 100 and 200 bases) and extending from the midpoint to end up with a fragment size of 73 bases. RPM normalized coverage was calculated on the 73 base fragments.
Genome_build: sacCer2
Supplementary_files_format_and_content: bigWig - rpm normalized coverage based on total bowtie2 alignments
|
| |
|
| Submission date |
Sep 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Madelaine Gogol |
| Organization name |
Stowers Institute
|
| Department |
Computational Biology Core
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE61210 |
Swi/Snf dynamics on stress responsive genes is governed by competitive bromodomain interactions. |
|
| Relations |
| BioSample |
SAMN03023815 |
| SRA |
SRX696012 |
