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Sample GSM1499619 Query DataSets for GSM1499619
Status Public on Oct 16, 2014
Title WT unstressed rep1 Snf2 INPUT for Snf2 N'ab
Sample type SRA
 
Source name yeast
Organism Saccharomyces cerevisiae
Characteristics genotype/variation: WT
tissue: WCE
antibody: INPUT
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 ChIP-Seq
Library source genomic
Library selection ChIP
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 SAMN03023803
SRA SRX696000

Supplementary file Size Download File type/resource
GSM1499619_input_wt_unstressed_rep1_nterm.bw 82.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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