 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 07, 2014 |
| Title |
G1_phase_synchronized_GCC biological replicate #2 |
| Sample type |
SRA |
| |
|
| Source name |
cdc10-129 (G1 phase) synchronized Schizosaccharomyces pombe
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: MY291
cell cycle: G1 phase
|
| Treatment protocol |
Synchronization cultures (125 ml EMM2, in baffled flasks) were inoculated with starter culture to an OD595 = ~0.05 and incubated (26°C, 120 rpm). Cultures were grown for four generations (OD595 ~0.8) before synchronization was induced by the addition of pre-warmed EMM2 medium (125 ml, 46°C), instantly rising the temperature of the culture to the restrictive temperature (36°C). Cultures were incubated in a hot water bath (36°C, 140 rpm, for 4 h) to complete synchronization.
|
| Growth protocol |
Schizosaccharomyces pombe strains were recovered from -80°C on YES (2% agar) plates (26°C, 4 days). YES medium (12 ml) starter cultures were inoculated and incubated (26°C, 200 rpm) until the OD595 measured ~0.8 (~24 h).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin isolation and GCC were performed as in Rodley et al. 2009 and Cagliero et al. 2013, with modifications; Following synchronization, cultures (200 ml) were cross-linked, washed, and suspended in FA-lysis buffer. Aliquots containing ~9.5*108 cells were made up to a volume of 330 μl with FA-lysis buffer and the cell walls were digested with T20 Zymolyase (70 μl at 75mg/ml; 35°C, 40 min with periodic inversion) before heat inactivation (60°C, 5 min). Acid washed glass beads (500 μl) were added to each sample before disruption in a Geno/Grinder (-20°C; 1,750 rpm, 2 x 30 sec on 60 sec off; SPEX sample prep 2010). Glass beads were removed by the centrifugation of chromatin through a pin hole into a clean tube (2,000 rpm, 1 min). Chromatin was pelleted (13,000 rpm, 15 min, 4°C), washed with FA-lysis buffer, suspended in chromatin digestion buffer and stored (-80°C).
AseI (100U, New England Biolabs, 37°C, 2 h). A ligation control (sees below and Supplementary Table S8) was added to the AseI digested chromatin, samples were diluted (~20-fold) and ligated with T4 DNA ligase (20U, Invitrogen). Following ligation, cross-links, protein and RNA were removed. pUC19 plasmid (27.4pg/2ml) was added as a sequence library preparation ligation control before phenol:chloroform (1:1) extraction and column purification.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Fission yeast cells synchronized in the G1 phase of the cell cycle
G1_combined_ra.out, G1_combined_ra.out.datmult
|
| Data processing |
Library strategy: Genome conformation capture
Paired-end reads were aligned using the SOAP algorithm not allowing any mismatches or unassigned bases (http://soap.genomics.org.cn/)
The dimensional interaction networks were constructed using the topography suit Rodley et al. 2009.
genome build: ASM294v2
|
| |
|
| Submission date |
Nov 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Justin M. O'Sullivan |
| E-mail(s) |
justin.osullivan@auckland.ac.nz
|
| Organization name |
University of Auckland
|
| Department |
Liggins Institute
|
| Street address |
85 Park Road, Grafton
|
| City |
Auckland |
| ZIP/Postal code |
1023 |
| Country |
New Zealand |
| |
|
| Platform ID |
GPL15167 |
| Series (2) |
| GSE52283 |
Global analyses of cell cycle dependent changes in fission yeast genome organization reveal correlations with alterations in transcript levels [GCC] |
| GSE52287 |
Global analyses of cell cycle dependent changes in fission yeast genome organization reveal correlations with alterations in transcript levels |
|
| Relations |
| BioSample |
SAMN02401725 |
| SRA |
SRX376698 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1262377_G1_rep2_2B_ra.out.dat.gz |
41.6 Mb |
(ftp)(http) |
DAT |
SRA Run Selector |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
