|
| Status |
Public on Aug 07, 2023 |
| Title |
SWI3_untreated_R2_input |
| Sample type |
SRA |
| |
|
| Source name |
W303
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
antibody: none
strain: W303
genotype: swi3[delta]; SWI3::LEU2; SNF2-3V5::HISMX
treatment: Input. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde
|
| Treatment protocol |
Spike-in cells from an SK1 strain harboring a SNF2-3V5 allele were added at a ratio of 1:5 to each sample prior to immunoprecipitation. IP samples were immunoprecipitated using anti-V5 agarose beads (see Morse et al., 2023 materials and methods for details).
|
| Growth protocol |
Cells were grown in YPD to late-log phase and split into two flasks. One flask was untreated and the other treated with 5 mM DTT. Two biological replicates were collected 1 hour post-treatment. Replicates were collected on separate days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in 1% formaldehyde, lysed in FA lysis buffer with beadbeating, chromatin was extracted by fractionation and sheared using a Bioruptor Pico (see Morse et al., 2023 materials and methods for further details).
DNA libraries were prepared using a NEXTflex Rapid DNA-Seq Kit 2.0 bundle.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Spike in normalization was performed according to SNP-ChIP pipeline from Vale-Silva et al., 2019
reads were aligned to the sacCer3 reference genome using Bowtie
MACS2 was used to generate bedGraph files for ChIP samples normalized to input
bedGraph files were adjusted by multiplying read depth at each position with the calculated SNP-ChIP normalization factor for each sample
Spike-in adjusted, normalized bedGraph files were converted to BigWig files using deeptools
Assembly: sacCer3 (R64)
Supplementary files format and content: BigWig (.bw) files scaled using SNP-ChIP spike-in normalization for visualization in IGV
|
| |
|
| Submission date |
Apr 15, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Elçin Ünal |
| E-mail(s) |
elcin@berkeley.edu
|
| Organization name |
UC Berkeley
|
| Street address |
628 Barker Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94706 |
| Country |
USA |
| |
|
| Platform ID |
GPL27812 |
| Series (2) |
| GSE229798 |
Regulation of transcriptional interference by the Swi/Snf complex [ChIP-seq] |
| GSE229952 |
Regulation of transcriptional interference by the Swi/Snf complex |
|
| Relations |
| BioSample |
SAMN34203529 |
| SRA |
SRX19979597 |
