 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 02, 2012 |
| Title |
12_1_d FAIRE-seq |
| Sample type |
SRA |
| |
|
| Source name |
yeast extract
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4716xRM11_1a segregant
|
| Treatment protocol |
The yeast cell was 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 cell was harvested by centrifugation at 3000 rpm for 5 minutes, and the pellet cells was rinsed twice with 10ml cold PBS and stored at -70ºC after removing all supernatant. Fixed cell was re-suspended in 300ul ChIP lysis buffer (50mM HEPES-KOH, pH7.5, 140mM NaCl, 1% Triton-X 100, 0.1% Sodium deoxycholate, 1mM EDTA) and protease inhibitor (Roche Inc. #1697498) per 0.12g of cells. Glass bead (425-600 micron diameter, Sigma #G8772) was added an equal volume to each sample and mixed 5 times 30 seconds by vortex mixer with 30 second incubation on ice. Then glass beads were filtered by puncture bottom of tube with a 20-26G needle and centrifugation. The samples were sonicated for 20 cycles (30 seconds ON and 30 seconds OFF) using a Bioruptor sonicator. DNA isolation was done by adding an equal volume of phenol-chloroform (Amresco. AMR-0883-2, phenol : chloroform : isoamyl alcohol 25:24:1), vortexing vigorously for 30 seconds and centrifuged at 13000 rpm for 10 minutes at 4ºC. The aqueous phase was isolated and the stored in a separate tube. The DNA was precipitated by addition of sodium acetate (final 0.3M) and two times the volume of 95% ethanol and incubated at -20ºC overnight. The precipitate was centrifuged at 13000 rpm for 20 minutes at 4ºC. Then the pellet was washed with 70% ethanol and dried at room temperature. The pellet was resuspended in dH2O with the addition of RNase A (final 100ug/mL), and then incubated at 37ºC for 2 hours. DNA fragments of 100-350 bp were eluted from 2% agarose gel.
|
| 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 with 200ml YPD medium in conical flask and incubated under shaking condition at 200 rpm overnight to 1.5 of the value of A600.
|
| 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
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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
|
| |
|
| Submission date |
Nov 03, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
kwoneel kim |
| E-mail(s) |
kwoneelkim@gmail.com
|
| Organization name |
KAIST
|
| Street address |
Gwahangno, Yuseong gu
|
| City |
Daejeon, Seoul |
| ZIP/Postal code |
305-701 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE33466 |
Open chromatin maps of genetically different yeast strains |
|
| Relations |
| SRA |
SRX104250 |
| BioSample |
SAMN00750060 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM827879_12_1_d.bed.gz |
16.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
