|
| Status |
Public on Apr 19, 2021 |
| Title |
S52A 0h polysomes-Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
S52A 0h polysomes
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: substitution of serine 52 of eIF2alpha by alanine
timepoint: at exponential phase (0 hours)
molecule subtype: mRNA extracted from polysomes
|
| Growth protocol |
Fission yeast cells were cultivated in YES medium at 30ºC until the reach OD550=0.5 (time 0 hours). They were cultivated for 6 additional hours (time 6 hours), time which coincides with early entry in stationary phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA and polysomal RNA were extracted as described in Swaminathan et al. 2006
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
S52-pol-0-expA
|
| Data processing |
Raw reads, in FASTQ format, were quality checked with FASTQC
Paired-end reads were aligned against Schizosaccharomyces pombe genome and sorted by coordinate position with STAR. Alignment files (BAM) were indexed with samtools
Aligned reads were assigned to Schizosaccharomyces pombe genes with function QC from QoRTs software package using default parameters for paired-end and strand-specific sequences
Normalization of read counts and differential expression was estimated with bioconductor package DESeq2 with default parameters
Genome_build: ASM294v2 Ensembl fungi release 35
Supplementary_files_format_and_content: Raw and normalized counts are placed in two separated sheets of an Excel file. Gene names and descriptions are also included.
|
| |
|
| Submission date |
Jul 28, 2020 |
| Last update date |
Apr 19, 2021 |
| Contact name |
Juan Carlos Oliveros |
| Organization name |
CNB, CSIC
|
| Street address |
Darwin 3
|
| City |
Cantoblanco |
| State/province |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17225 |
| Series (1) |
| GSE155256 |
Specific translation during aging mediated by phosphorylation of Schizosaccharomyces pombe eIF2alpha |
|
| Relations |
| BioSample |
SAMN15659844 |
| SRA |
SRX8838528 |
