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| Status |
Public on May 01, 2017 |
| Title |
pGal1-Ndt80-myc_2 |
| Sample type |
SRA |
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| Source name |
W303 a-cell
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
media condition: Sraffinose + 1.7% galactose
chip antibody: human c-myc
strain number: yIN219
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| Growth protocol |
Cells were grown overnight in Sraffinose, diluted back to OD = 0.02 in Sraffinose and grown for 15 hours, then galactose (1.7% total) was added and cells were grown for 5 hours.
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| 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)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Quality analysis performed with FastQC
ChIP-seq reads were aligned to the S. cerevisiae genome assembly using bowtie2 and default parameters
Files were converted to sorted .bam files using Samtools
Peak separation distance was determined using the binding.characteristics function in the SPP package in R
Peaks and fold enrichment were calculated using MACS2, using peak separation distances calculated from SPP and --nomodel parameter
Genome_build: S. cerevisiae genome was downloaded from the Candida Gene order Browser in May 2015
Supplementary_files_format_and_content: bedGraph.wig files were generated from indexed, sorted .bam file using genomeCoverageBed tool in BedTools, followed by a .bed to .wig conversion script in Python. FE.bdg.wig files were generated by MACS2 using the -SPMR parameter, and converted to .wig using the same Python script. Peaks.xls files were generated for experiments with tagged proteins using untagged strains as a control in MACS2.
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| Submission date |
Nov 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Isabel Nocedal |
| Organization name |
UCSF
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| Street address |
600 16th St.
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL21656 |
| Series (1) |
| GSE90660 |
ChIP-Seq of constitutively expressed Ndt80-Myc in S. cerevisiae |
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| Relations |
| BioSample |
SAMN06068121 |
| SRA |
SRX2381671 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2410145_Scer_Tag2.bedGraph.wig.gz |
36.4 Mb |
(ftp)(http) |
WIG |
| GSM2410145_Scer_Tag2_FE.bdg.wig.gz |
31.2 Mb |
(ftp)(http) |
WIG |
| GSM2410145_Scer_Tag2_peaks.xls.gz |
25.5 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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