|
| Status |
Public on Oct 28, 2016 |
| Title |
rnh1∆rnh201∆_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
poly(A) selected RNA of rnh1∆rnh201∆
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: rnh1-delta-rnh201-delta
strain: p2880
|
| Treatment protocol |
RNA was isolated from the strains using TRI Reagent (Sigma Aldrich) following the manufacturer's instructions.
|
| Growth protocol |
30ºC liquid cultures grown to log phase in full media (YEA) for the WT and rnh1∆rnh201∆ samples, and in SCD-Th for Pnmt::rnh1 ON and SDC+Th for Pnmt::rnh1 OFF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The samples were reverse transcribed to cDNA using the SuperScriptTM Indirect cDNA labeling system (Life Technologies) with anchored oligo(dT)20.
|
| Label |
Cy5
|
| Label protocol |
The cDNAs from WT and mutant strains were labeled with Cy3 (WT or OFF state) and Cy5 (mutant or ON state) (GE Healthcare).
|
| |
|
| Channel 2 |
| Source name |
poly(A) selected RNA of wildtype
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: wildtype
strain: p2494
|
| Treatment protocol |
RNA was isolated from the strains using TRI Reagent (Sigma Aldrich) following the manufacturer's instructions.
|
| Growth protocol |
30ºC liquid cultures grown to log phase in full media (YEA) for the WT and rnh1∆rnh201∆ samples, and in SCD-Th for Pnmt::rnh1 ON and SDC+Th for Pnmt::rnh1 OFF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The samples were reverse transcribed to cDNA using the SuperScriptTM Indirect cDNA labeling system (Life Technologies) with anchored oligo(dT)20.
|
| Label |
Cy3
|
| Label protocol |
The cDNAs from WT and mutant strains were labeled with Cy3 (WT or OFF state) and Cy5 (mutant or ON state) (GE Healthcare).
|
| |
|
| |
| Hybridization protocol |
Hybridization, blocking, and washing was performed following the Agilent instructions.
|
| Scan protocol |
Scanning of arrays was performed using Agilent DNA Microarray Scanner and Agilent Scan control software (v A.8.4.1.).
|
| Data processing |
Agilent Feature Extraction Software (v 10.7.3.1) Protocol: GE2_107_Sep09 with modifications; Background Subtraction Method - Local Background; Detrend on Replicates Only - False; Robust Neg Ctrl Stats? - True; Choose universal error, or the most conservative - Use Universal Error Model; Dye Normalization Probe Selection Method/Variable Rank Tolerance - True; Max Number Ranked Probes - -1; Normalization Correction Method - Lowess Only; Spikein Target Used - False p-value filtering (p<=0.05) and background filtering (BG=median of negative control probes for green channel and red channel, probes with gProcessedSignal < 2x gBG AND rProcessedSignal < 2x rBG are filtered out) Filtered probes value set to 1.
The bedGraph files were generated in R, using custom scripts. They contain the final, normalized values that are included in the Sample data tables.
|
| |
|
| Submission date |
Jul 26, 2016 |
| Last update date |
May 27, 2018 |
| Contact name |
Tamas Fischer |
| E-mail(s) |
[email protected]
|
| Organization name |
The Australian National University
|
| Department |
The John Curtin School of Medical Research
|
| Lab |
Fischer group
|
| Street address |
Building 131, Garran Rd
|
| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19654 |
| Series (2) |
| GSE84882 |
Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair |
| GSE84883 |
Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair |
|
