|
| Status |
Public on May 20, 2015 |
| Title |
ctr1Δ |
| Sample type |
SRA |
| |
|
| Source name |
rRNA depleted RNA of ctr1Δ
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: deletion strain: ctr1-delta (p1135)
|
| Treatment protocol |
NA
|
| 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 |
RNA was isolated from either wildtype strains or deletion mutants using TRI Reagent (Sigma Aldrich) following the manufacturers instructions
Ribosomal RNAs were depleted from Turbo DNase-treated total RNAs using a Ribo-zero Magnetic Gold Kit (Epicentre). The cDNA libraries were prepared using NEBNext Ultra RNA Directional Library Prep Kit (NEB) according to the manufacturer’s instructions. The libraries were purified with Agencourt AMPure XP beads (Beckman Coulter) and assessed on a Bioanalyzer (Agilent). Subsequently, 2x100 bp paired-end sequencing was performed on an Illumina HiSeq 2000 sequencer at BGI Tech (Hong Kong).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
rRNA depleted RNA
|
| Data processing |
fastq files were mapped using tophat-2.0.13
coverage was calculated for fw and rev strand separately
median coverage was calculated for all non-intron containing genes, and the median non-intron coding gene coverage was calculated for each dataset
datasets were normalized using the median non-intron containing gene coverage (set to 100)
Genome_build: Schizosaccharomyces_pombe_Ensembl_EF2
Supplementary_files_format_and_content: fw.BigWig and rev.BigWig files for each dataset describe the normalized RNA coverage at the fw/rev strand
|
| |
|
| Submission date |
Jan 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tamas Fischer |
| E-mail(s) |
tamas.fischer@bzh.uni-heidelberg.de
|
| Phone |
+49 6221 544728
|
| Organization name |
Biochemie Zentrum Heidelebrg
|
| Department |
BZH
|
| Lab |
AG Fischer
|
| Street address |
Im Neuenheimer Feld 328
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13988 |
| Series (2) |
| GSE64991 |
The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome [RNA-Seq] |
| GSE64992 |
The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome |
|
| Relations |
| BioSample |
SAMN03284845 |
| SRA |
SRX844151 |
