|
| Status |
Public on Sep 24, 2012 |
| Title |
WT_25C |
| Sample type |
SRA |
| |
|
| Source name |
Whole colony
|
| Organism |
Schizophyllum commune |
| Characteristics |
parental strain: Cross of H4-8 and H4-8b
deleted gene: wild-type
|
| Growth protocol |
Colonies were grown from plug inoculum. Plugs of the compatible monokaryons were placed next to each other. Cultures were incubated for 6 days at 25 degrees C in continuous light. After this period, samples indicated with "42C" were placed at 42C for 1 hour. After that, they were placed back at 25C for 5 hours. Then RNA was isolated from each of the colonies.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Three biological replicates were pooled. Colonies were frozen in liquid nitrogen and powdered. Total RNA was isolated using the Trizol reagent. The quality of the RNA was analysed on a RNA 6000 Lab-on-a-Chip using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). The Illumina mRNA-Seq Sample Prep Kit was used to process the samples. The sample preparation was performed according the Illumina protocol "Preparing Samples for Sequencing of mRNA" (1004898 Rev. D).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
The sequenced reads were mapped to the genome sequence using the program Tophat 1.0.13 and Bowtie 0.12.5, using default settings with the exception of the minimum and maximum intron length (10 and 400 bp, respectively).
|
| |
|
| Submission date |
Sep 07, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
H.A.B. Wösten |
| Organization name |
Utrecht University
|
| Street address |
Padualaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL10795 |
| Series (1) |
| GSE24007 |
Genome-wide expression analysis of dikaryotic colonies of Schizophyllum commune under various conditions: wild-type, delta-wc2, delta-wc2 hsp3(pr)-wc2 |
|
| Relations |
| SRA |
SRX026386 |
| BioSample |
SAMN00110492 |
