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Sample GSM968695 Query DataSets for GSM968695
Status Public on Feb 28, 2013
Title Chd1 WT input 10' MNase (Chd1IN 20120223 6)
Sample type SRA
 
Source name Chd1 wildtype input
Organism Saccharomyces cerevisiae
Characteristics sample type: nuclei
chip antibody: input
strain: W1588-4C (congenic to W303-1A except RAD5+)
genotype: Chd1 WT
Extracted molecule genomic DNA
Extraction protocol Chd1 wildtype input after 10' micrococcal nuclease followed by sequencing
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 2000
 
Description Chd1 wildtype input after 10' micrococcal nuclease followed by sequencing
Data processing 1. We used Novoalign (2.07.00MT - Aug 5 2010) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file .sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.
Genome_build: sacCer3
Supplementary_files_format_and_content: wig
 
Submission date Jul 17, 2012
Last update date May 15, 2019
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platform ID GPL13821
Series (2)
GSE39331 Dynamics of yeast ISWI and CHD chromatin remodeler genomic association
GSE39431 Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)
Relations
BioSample SAMN02197485
SRA SRX1625713

Supplementary file Size Download File type/resource
GSM968695_Chd1IN_20120223_6.wig.gz 48.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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