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| Status |
Public on Nov 02, 2012 |
| Title |
BY4716 FAIRE-seq |
| Sample type |
SRA |
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| Source name |
yeast extract
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4716
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| Treatment protocol |
The yeast cells were fixed by 37% formaldehyde (final 1%) for 20 minutes at room temperature. To stop fixation, 2.5M glycine (final 125 mM) was added and mixed swirling for 5 minutes at room temperature. The fixed cells were harvested by centrifugation at 3000 rpm for 5 minutes, and the pellet cells were rinsed twice with 10ml cold PBS and stored at -70ºC after removing all supernatant. The fixed cells were resuspended in ChIP lysis buffer (50mM HEPES-KOH, pH7.5, 140mM NaCl, 1% Triton-X 100, 0.1% Sodium deoxycholate, 1mM EDTA) containing protease inhibitor (Roche Inc. #1697498). 300ul of ChIP lysis buffer was used for 0.12g of fixed cells. For disruption of cells, the same volume of glass beads (425-600 micron diameter, Sigma #G8772) was added to each sample and five repetitions of 30-second vortexing and 30-second incubation on ice were carried out. Cells were selectively filtered by spinning at 1000G for 3 minutes at 4ºC after piercing to the bottom of the tube using a 20-26G needle. The samples were then sonicated for 20 cycles (30 seconds ON and 30 seconds OFF) using a Bioruptor sonicator at a “high” mode. DNA isolation was done by the addition of an equal volume of phenol-chloroform (Amresco. AMR-0883-2, phenol : chloroform : isoamyl alcohol 25:24:1), vortexing vigorously for 30 seconds, and spinning at 13000 rpm for 10 minutes at 4ºC. The aqueous phase was isolated and stored in a separate tube. The DNA was precipitated by addition of sodium acetate (final 0.3M) and the 2x volume of 95% ethanol and then incubated at -20ºC for 2 hours. The precipitate was centrifuged at 13000 rpm for 20 minutes at 4ºC. The pellet was washed with 70% ethanol and dried at room temperature. The pellet was resuspended in dH2O and treated with RNaseA (final 100ug/mL), followed by incubation at 37ºC for 2 hours. DNA fragments of 100-350 bp were eluted from 2% agarose gel.
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| Growth protocol |
We obtained the BY-RM cross strains from the original authors (Science 296, 752-755 & PNAS 102, 1572-1577). Each yeast strain was grown in 200ml YPD medium and incubated with shaking at 200 rpm overnight to an A600 value of 1.5.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
High-throughput sequencing of the 96 FAIRE libraries was performed on eight lanes of a single flow cell of HiSeq 2000 with 100 bp run length. Illumina’s Multiplexing Sample Preparation Oligonucleotide Kit was used to sequence twelve samples in each lane.
library_strategy: FAIRE-seq
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Raw data processing was carried out by means of Illumina data pipeline (ELAND and CASAVA). To identify the peaks of the reads, we ran F-seq with the default parameters. Small-sized peaks (< 15 bp) were extended in both directions such that all the peaks are 15 bp long at least. To identify all possible open chromatin regions (OCRs), we merged the extended peak positions of the 96 yeast strains by using BEDTools. Overlapping peaks were merged into a single peak.
Genome build: sacCer2
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| Submission date |
Nov 03, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
kwoneel kim |
| E-mail(s) |
kwoneelkim@gmail.com
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| Organization name |
KAIST
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| Street address |
Gwahangno, Yuseong gu
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| City |
Daejeon, Seoul |
| ZIP/Postal code |
305-701 |
| Country |
South Korea |
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| Platform ID |
GPL13821 |
| Series (1) |
| GSE33466 |
Open chromatin maps of genetically different yeast strains |
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| Relations |
| SRA |
SRX104237 |
| BioSample |
SAMN00750047 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM827866_BY4716.bed.gz |
15.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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