|
| Status |
Public on Mar 26, 2024 |
| Title |
Control Lsm3-TAP R3_2h |
| Sample type |
SRA |
| |
|
| Source name |
BY4742
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
genotype: Wt
chip antibody: IgG
time (hrs): 2
|
| Growth protocol |
For experiments using cells at different growth phases, single colonies of Saccharomyces cerevisiae BY4742 cells were inoculated into 10 ml of YPD medium (1% yeast extract, 2% bacto-peptone and 2% glucose), precultivated in YPD at 30 ◦C, diluted in fresh YPD to an OD600nm of 0.1 to 0.15 and cultivated for 2 h at 30 ºC after which the first samples (labelled 0 h in the figures) were harvested. Subsequent samples were harvested at 2 h, 4 h and 6 h after the 0 h point
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lysis and separation of chromatin fractions were performed using the standard protocol Svejstrup et al., (2003), except that we used ammonium sulfate to 0.5 M final concentration instead of 1 M to release chromatin-associated proteins, as we have described previously
DNA fragments were then cleaned using the ChIP DNA clean & concentratorTM kit (ZYMO RESEARCH). Aliquots of 1 to 2 ng of DNA from each sample were tested for proper shearing using a fragment analyzer (Agilent 2100 Bioanalyzer G2938C), and then sent for library preparation using the SMARTer ThruPLEX kit and subsequent pair-ended sequencing using Illumina NovaSeq S4-200 cycle flow cells in individual lanes.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina iSeq 100 |
| |
|
| Description |
Control for Lsm3 2 h Rep3
|
| Data processing |
Reads were mapped using Bowtie2 to the sacCer3 reference genome. After mapping of reads, we called narrow peaks at an average fragment size of 300 bp and an FDR value < 0.05
ChIP-seq using an untagged wild type strain was used as control for peak calling and enrichment analyses
Assembly: sacCer3
Supplementary files format and content: bigwig files (narrow peaks)
|
| |
|
| Submission date |
Jan 31, 2024 |
| Last update date |
Mar 26, 2024 |
| Contact name |
ALEXANDER VERGARA |
| E-mail(s) |
vergara.alexander@gmail.com
|
| Organization name |
Umea University
|
| Department |
Physics
|
| Lab |
IceLab
|
| Street address |
Historiegrand 9, 1002
|
| City |
Umea |
| ZIP/Postal code |
90734 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL34156 |
| Series (2) |
| GSE254759 |
Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes [ChIP-seq] |
| GSE254761 |
Growth regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes |
|
| Relations |
| BioSample |
SAMN39711360 |
| SRA |
SRX23485665 |
