|
| Status |
Public on Jan 01, 2016 |
| Title |
WT A |
| Sample type |
SRA |
| |
|
| Source name |
wild type
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: wild type
|
| Treatment protocol |
30 degrees, harvested during logaritmic phase, O.D. 0,5 - 1
|
| Growth protocol |
YEA liquid medium - Yeast Extract + Casaminacids + Adenine + Glucose
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot Phenol RNA extraction, Qiagen RNA-easy clean up
Poly-A enrichment using oligo(dT) beads. cDNA synthesis using Invitrogen Supercript III. Incorporation of dUTP on second strand. Standard Illumina library preparation protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
h- L972
|
| Data processing |
Qualitycontrolled, filtered and trimmed using FASTX-Toolkit Hannon Lab
Aligment against S. Pombe genome EF2 using Bowtie 0.12.7
Differential Expression using DEseq
Genome_build: S. Pombe EF2
Supplementary_files_format_and_content: Microsoft Excel, Differential expression data with baseMeanA as wt control and baseMeanB as corresponding mutant strain.
|
| |
|
| Submission date |
Oct 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jonas Carlsten |
| E-mail(s) |
jonas.carlsten@gu.se
|
| Organization name |
University of Gothenburg
|
| Department |
Biomedicin
|
| Lab |
Claes Gustafsson
|
| Street address |
Medicinaregatan 9A
|
| City |
Göteborg |
| ZIP/Postal code |
413 91 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13988 |
| Series (1) |
| GSE73792 |
Comparison of RNA profiling between wild type, med20∆, rrp6∆ and med20∆/rrp6∆ in Schizosaccharomyces pombe |
|
| Relations |
| BioSample |
SAMN04147851 |
| SRA |
SRX1309144 |
