 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 22, 2020 |
| Title |
Bud27-TAP Input 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bud27-TAP Input
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: BY4741
genotype/variation: containing a tap-tagged version of Bud7
immunopreciatation: input
|
| 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 for a BY4147 wild-type strain containing a tap-tagged version of Bud7 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. Immunoprecipitation was performed in duplicate using 200 µl of magnetic beads (Dynabeads Pan Mouse IgG, Invitrogen) and 300 µl of the sonicated sample. Washing and de-crosslinking followed the conventional chromatin immunoprecipitation procedure; supernatants were collected in the same tube and DNA was purified with the Nucleospin Extract II Purification kit (Macherey-Nagel). The eluted DNA was concentrated by lyophilization. Input and immunoprecipitated DNAs were sequenced in an Illumina HiSeq 2000 instrument
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 |
BT2i_17634_ACTTGA
|
| 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 |
May 17, 2019 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Francisco Navarro |
| E-mail(s) |
fngomez@ujaen.es
|
| 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) |
| GSE131388 |
Genome-wide maps of Bud27 binding to the chromatin [ChIP-seq] |
| GSE131390 |
Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae |
|
| Relations |
| BioSample |
SAMN11668099 |
| SRA |
SRX5854416 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3772982_BT2i.bw |
11.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
