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Sample GSM968687 Query DataSets for GSM968687
Status Public on Feb 28, 2013
Title Chd1 K407R N-ChIP-seq 2.5' MNase (K407R Chd1 FLAG 20120606 2)
Sample type SRA
 
Source name Chd1 K407R ChIP
Organism Saccharomyces cerevisiae
Characteristics sample type: nuclei
chip antibody: FLAG (Sigma anti-FLAG M2 magnetic beads, catalog #8823, lot #041M6135)
strain: W1588-4C (congenic to W303-1A except RAD5+)
genotype: Chd1 K407R
Extracted molecule genomic DNA
Extraction protocol Chd1 K407R native chromatin immunoprecipitation after 2.5' micrococcal nuclease followed by sequencing
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Chd1 K407R native chromatin immunoprecipitation after 2.5' 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
GSE39430 Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1)
Relations
SRA SRX160481
BioSample SAMN01090677

Supplementary file Size Download File type/resource
GSM968687_K407R_Chd1_FLAG_20120606_2.wig.gz 68.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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