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Sample GSM2832772 Query DataSets for GSM2832772
Status Public on Mar 05, 2019
Title Wild-type Total Input DNA Seq
Sample type SRA
 
Source name input_wildtype
Organism Saccharomyces cerevisiae
Characteristics strain: ROY4825 W-303
genotype: MATa SCC2-13xMyc::KanMX ADE2 his3-11,15 leu2-3, 112 lys2D trp1-1 ura3-1
chip antibody: none (input)
Growth protocol Cells were grown to early log phase in 300ml YPD
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde, quenched, lysed and sonicated to generate small DNA fragments. ChIPs were performed with 5ug of 9E10 from Covance (now Biolegend).
Libraries were prepared at the Functional Genomics Laboratory, UC Berkeley and sequenced at the Vincent J Coates Sequencing Laboratory at UC Berkeley.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Description Total Input DNA
Data processing Sequencing data were mapped to the S. cerevisiae reference genome sacCer3, using bowtie2 (Langmead and Salzberg, Nature Methods, 2012) with the default settings.
The typical DNA fragment length was estimated based on strand cross-correlation maxima using the SPP package (Kharchenko et al., Nat Biotechnol., 2008) (available at https://github.com/hms-dbmi/spp/).
The reads were extended to the estimated typical fragment size of 170 bp and genome-wide coverage profiles were computed in MATLAB. The coverage profiles were normalized such that the average coverage for every chromosome is 1.
IGV tracks (tdf files) were generated using igvtools.
Genome_build: sacCer3
Supplementary_files_format_and_content: tdf files containing the normalized occupancy profiles, for the IGV browser
 
Submission date Oct 26, 2017
Last update date May 15, 2019
Contact name Razvan V. Chereji
E-mail(s) razvan.chereji@nih.gov
Phone 301-435-8670
Organization name National Institutes of Health
Department NICHD
Lab David J. Clark Lab
Street address 6 Center Drive, Room 2A14
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platform ID GPL21656
Series (2)
GSE106249 Transfer RNA Genes Affect Chromosome Architecture and Function [ChIP-seq]
GSE106250 Transfer RNA Genes Affect Chromosome Architecture and Function
Relations
BioSample SAMN07839699
SRA SRX3334032

Supplementary file Size Download File type/resource
GSM2832772_ROY4825_Scc2_Input.tdf 46.9 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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