|
| Status |
Public on May 20, 2015 |
| Title |
rrp6Δ-2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
rRNA depleted RNA of rrp6Δ
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: rrp6Δ
strain: p74
|
| Treatment protocol |
RNA was isolated from either wildtype strains or deletion mutants using TRI Reagent (Sigma Aldrich) following the manufacturers instructions
|
| Growth protocol |
WT and gene deletion strains were grown in YEA at 30°C to OD 0.5~0.8. Temperature sensitive strains were grown in YEA at 23°C to OD 0.3~0.4 and then moved to 37°C and grown for 4 h to OD<0.8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosomal RNA was depleted from total RNA extracts of all strains using a mixture of 5' biotinylated rRNA probes. The rRNA-depleted samples were reverse transcribed to cDNA using the SuperScriptTM Indirect cDNA labeling system (Life Technologies) with anchored oligo(dT)20 and random hexamers.
|
| Label |
Cy5
|
| Label protocol |
The cDNAs from WT and mutant strains were labeled with Cy3(WT) and Cy5(mutant) (GE Healthcare)
|
| |
|
| Channel 2 |
| Source name |
rRNA depleted RNA of wildtype
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: wildtype
strain: p20
|
| Treatment protocol |
RNA was isolated from either wildtype strains or deletion mutants using TRI Reagent (Sigma Aldrich) following the manufacturers instructions
|
| Growth protocol |
WT and gene deletion strains were grown in YEA at 30°C to OD 0.5~0.8. Temperature sensitive strains were grown in YEA at 23°C to OD 0.3~0.4 and then moved to 37°C and grown for 4 h to OD<0.8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosomal RNA was depleted from total RNA extracts of all strains using a mixture of 5' biotinylated rRNA probes. The rRNA-depleted samples were reverse transcribed to cDNA using the SuperScriptTM Indirect cDNA labeling system (Life Technologies) with anchored oligo(dT)20 and random hexamers.
|
| Label |
Cy3
|
| Label protocol |
The cDNAs from WT and mutant strains were labeled with Cy3(WT) and Cy5(mutant) (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 Substraction 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
|
| |
|
| Submission date |
Jan 14, 2015 |
| Last update date |
May 20, 2015 |
| 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) |
| GSE64979 |
The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome [expression array] |
| GSE64992 |
The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome |
|
