|
| Status |
Public on Dec 12, 2018 |
| Title |
WT_glyc_R2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole cell
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Y44_Wild Type
genotype: h-
|
| Growth protocol |
Cells were cultured in YES 3% glucose for four hours at 32 degrees before being collected by centrifugation, washed twice in sterile water and shifted to YES 3% glucose, YES 3% sucrose, YES 3% glycerol + 0.1% glucose or YES 3% glycerol and cultured at 32 degrees for a further four hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested by centrifugation and the hot phenol method (Lyne et al. 2003, BMC Genomics 4:27) was used to isolate total RNA from cells
Libraries for R72, R73, R74, R81 and R82 were prepared from ribo-depleted RNA using the Illumina TruSeq unstranded protocol. All other samples were prepared from ribo-depleted RNA using the Illumina TruSeq stranded protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: scr1_counts_combined.csv
processed data file header: R110
|
| Data processing |
basecalls were performed using Illumina CASAVA v1.8.4 pipeline
raw reads were cleaned using Cutadapt v1.9.1 with default parameters and assessed for quality using FastQC
cleaned reads were aligned to the S. pombe ASM294v2.25 genome using Tophat2 v2.1.1 with a max intron size of 5000bp and library-type of fr-firststrand (for stranded samples) or fr-unstranded (for unstranded samples)
reads mapping to gene features were counted with featureCounts v1.5.2 using -s 2 (for stranded samples)
Differential gene expression was performed using DESeq2 v1.12.3
Genome_build: ASM294v2
Supplementary_files_format_and_content: csv file includes read counts for each sample
|
| |
|
| Submission date |
Dec 11, 2018 |
| Last update date |
Dec 14, 2018 |
| Contact name |
Dane Aaron McKay Vassiliadis |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Melbourne
|
| Street address |
Parkville VIC 3000
|
| City |
Melbourne |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17225 |
| Series (2) |
| GSE123617 |
A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe [RNA-seq] |
| GSE123633 |
A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe |
|
| Relations |
| BioSample |
SAMN10580263 |
| SRA |
SRX5125030 |
