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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 16, 2014 |
| Title |
WT stressed rep1 INPUT |
| Sample type |
SRA |
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| Source name |
yeast
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: WT
tissue: WCE
antibody: INPUT
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| Treatment protocol |
To induce stress cells grown in YPD were shifted to YNB + 0.5% dextrose
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| Growth protocol |
Cells were grown in YPD
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| 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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
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| 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
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| Submission date |
Sep 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Madelaine Gogol |
| Organization name |
Stowers Institute
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| Department |
Computational Biology Core
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| Street address |
1000 E. 50th Street
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| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platform ID |
GPL17143 |
| Series (1) |
| GSE61210 |
Swi/Snf dynamics on stress responsive genes is governed by competitive bromodomain interactions. |
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| Relations |
| BioSample |
SAMN03023841 |
| SRA |
SRX695982 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1499601_input_wt_stressed_rep1.bw |
99.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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