|
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 |