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| Status |
Public on Jun 24, 2021 |
| Title |
ha-fast1a-wt-h202T68-x18 |
| Sample type |
SRA |
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| Source name |
budding yeast
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
antibody: ha
background: wt
treatment: h202T68
sensor: H3-Fast
strain: YGY559
genotype: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1
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| Treatment protocol |
For h2o2 samples: exponentially growing cultures were exposed to 0.3 mM H2O2 and samples taken at indicated timepoints (in minutes)
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| Growth protocol |
yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for 6 hours at 30deg before fixation
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail), and SLIM-ChIP protocol was carried continued as in Gutin et al.
SLIM-Chip, as per Gutin et al, Cell Reports 2019
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
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| Data processing |
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-170 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2
Supplementary_files_format_and_content: *.out file contains gneome coverage for all 12,157,105 bases in the yeast genome in one column (chromosomal order 1-16,Mitochondrion)
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| Submission date |
Oct 29, 2020 |
| Last update date |
Jun 25, 2021 |
| Contact name |
Naama Barkai |
| Organization name |
Weizmann Institute
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| Department |
Molecular Genetics
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| Lab |
Barkai Lab
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| Street address |
Herzl St 234
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| City |
Rehovot |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platform ID |
GPL26302 |
| Series (1) |
| GSE157402 |
Nucleosome exchange in budding yeast |
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| Relations |
| BioSample |
SAMN16595602 |
| SRA |
SRX9399030 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4872780_ha-fast1a-wt-h202T68-x18.out.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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