|
| Status |
Public on Jul 06, 2015 |
| Title |
Ste12-myc_3 |
| Sample type |
SRA |
| |
|
| Source name |
a cell
|
| Organism |
Kluyveromyces lactis |
| Characteristics |
media condition: phosphate-starvation
chip antibody: human c-myc
|
| Growth protocol |
Cells were grown overnight for 14 h in YEPD, washed, then resuspended to OD=0.25 in phosphate starvation SD media for 2 hours, then induced with K. lactis alpha factor for 2 hours
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed with glass bead vortexing, sonicated for 3 15-minute cycles, and immunoprecipitated at 4˚C overnight
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 |
Quality analysis was performed using FastQC
Files were indexed and aligned to the K. lactis genome using bowtie2
Files were converted to .bam format using samtools
Peak separation distance was determined using the binding.characteristics function in the SPP package in R
Peaks were called using macs2
Genome_build: The K. lactis genome was downloaded from the Yeast Gene Order Browser in August 2014
Supplementary_files_format_and_content: bedGraph files were converted from bam files using the script genomeCoverageBed
|
| |
|
| Submission date |
Feb 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Trevor Sorrells |
| E-mail(s) |
trevorsorrells@gmail.com
|
| Organization name |
University of California, San Francisco
|
| Department |
Biochemistry and Biophysics
|
| Lab |
Johnson
|
| Street address |
600 16th St N374
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL19759 |
| Series (1) |
| GSE65792 |
K. lactis Ste12-myc ChIP-Seq in pheromone-responding a cells |
|
| Relations |
| BioSample |
SAMN03339145 |
| SRA |
SRX871231 |
