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Sample GSM1943648 Query DataSets for GSM1943648
Status Public on Jan 11, 2016
Title Untagged Opaque Cell Control 3 (136C)
Sample type SRA
 
Source name opaque cell
Organism Candida albicans
Characteristics media condition: SD+aa+Uri, 25°C
chip antibody: Living Colors Full-Length GFP Polyclonal
cell type: Opaque
genotype: WOR4 / WOR4
strain: AHY136
Treatment protocol Cells were crosslinked for 15 minutes with Formaldehyde (1% of final volume)
Growth protocol Room temperature SD+aa+Uri overnights were started from 5 to 7 day old colonies. Cultures were diluted back to 200mL at A600= 0.067 in the morning and allowed to regrow at 25°C to an OD600 of ~0.4.
Extracted molecule genomic DNA
Extraction protocol Cells were lysed with glass bead vortexing for 2 hours, sonicated for 2 15-minute cycles (30s on, 60s off), and immunoprecipitated at 4˚C overnight (5µL of Living Colors Full-Length GFP Polyclonal Antibody (Clontech 632592), Protein A-Sepharose 4B Fast Flow (Sigma P9424)).
Libraries were prepared using the NEBNext ChIP-Seq library prep kit for Illumina (New England Biolabs)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Files were indexed and aligned to the C. albicans genome using Bowtie2 with the default parameters
Files were converted to .bam format using samtools
Peak separation distance was determined using the binding characteristics function in the SPP R Bioconductor package
Peaks were called using Macs2
Genome_build: The C. albicans genome A21-s02-m09-r02 was downloaded from the Candida Genome Database on April 6, 2014
Supplementary_files_format_and_content: bedGraph files were converted from bam files using the script genomeCoverageBed
 
Submission date Nov 18, 2015
Last update date May 15, 2019
Contact name Matthew Lohse
Organization name BioSynesis, Inc.
Street address 44 Vicksburg Street
City San Francisco
State/province CA
ZIP/Postal code 94114
Country USA
 
Platform ID GPL19036
Series (1)
GSE75124 Identification and characterization of Wor4, a new transcriptional regulator of white-opaque switching
Relations
BioSample SAMN04284652
SRA SRX1441648

Supplementary file Size Download File type/resource
GSM1943648_136C-Calb_alignment.sort.bedgraph.gz 9.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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