 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 22, 2020 |
| Title |
BYc2: WT chip 2 |
| Sample type |
SRA |
| |
|
| Source name |
yeast culture
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
|
| Treatment protocol |
Crosslinked by adding 1% formaldehyde to the culture, during 15 minutes.After a 15-minute incubation, 10 ml of 2.5 M glycine were added and the culture was incubated for 5 min in the presence of this solution. Cells were harvested and washed 4 times with 150 mM NaCl, 20 mM Tris-HCl, pH 7.5. Then they were resuspended in 300 µl of lysis buffer (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, pH 8, 1% (v/v) Triton-X-100, 0.1% (w/v) sodium deoxycholate, 1 mM PMSF, 0.15% (w/v) benzamidine, and protease inhibitor cocktail (Complete, Roche)).
|
| Growth protocol |
200 ml of yeast culture were collected at an OD600 of about 0.6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell disruption was carried out by vigorously vortexing this sample in the presence of 200 µl of glass beads for 15 min. After disruption, lysis buffer was added to the cells extract to adjust 1.5 ml and then samples were subsequently sonicated by a Bioruptor sonicator (Diagenode) for 45 min at 30 s on/off intervals.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Immunoprecipitation was performed using 200 µl of magnetic beads Dynabeads M-280 Sheep anti-Mouse IgG (Invitrogen) mixed with 8WG16 anti-Rpb1 antibody (Santacruz), for Rpb1, and 300 µl of the sonicated sample.
|
| Data processing |
Input DNAs were sequenced in an Illumina HiSeq 2000 instrument.
The quality metrics of the Fastq sequencing datasets were obtained with FastQC and inspected visually
Sequencing adapters were removed from raw reads with Fastx Clipper
The resulting high-quality sequences were mapped to the S. cerevisiae S288c genome (SGD R64) with Hisat2
Supplementary_files_format_and_content: RPKM-normalised coverage bigWig tracks for the individual ChIP-seq datasets.
|
| |
|
| Submission date |
Jul 19, 2019 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Francisco Navarro |
| E-mail(s) |
[email protected]
|
| Phone |
0034953212771
|
| Organization name |
Universidad de Jaén
|
| Department |
Experimental Biology
|
| Lab |
Genetic
|
| Street address |
Campus Las Lagunillas s/n.
|
| City |
Jaén |
| State/province |
Jaén |
| ZIP/Postal code |
23071 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE131390 |
Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae |
| GSE134534 |
Genome-wide binding of Rpb1 (the largest subunit of the RNA polymerase II) to the chromatin state in bud27∆ and wild-type mutant strains (ChIP-seq) |
|
| Relations |
| BioSample |
SAMN12321474 |
| SRA |
SRX6473469 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3955258_BYc2.bw |
6.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
