|
| Status |
Public on Apr 12, 2017 |
| Title |
RNA_wild_type |
| Sample type |
SRA |
| |
|
| Source name |
wild type
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain number: 65
target molecule: total RNA
|
| Growth protocol |
cells were grown in liquid, rich YES medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
Total RNA was isolated applying the hot phenol method. The extracted nucleic acids were treated with DNAse I for 2 h at 37°C. DNAse was removed by a second phenol-chloroform-isoamylalcohol extraction and ethanol precipitation. 1 µg total RNA was degraded with Terminator nuclease (Epicentre) in buffer A at 30°C for 2 h.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichments were calculated with our house Perl scripts
Normalisation to reads per million for siRNA and ChIP experiments, normalisation to reads mapping to protein coding genes for RNAseq /RIPseq
Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv
|
| |
|
| Submission date |
Jan 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Mario Halic |
| E-mail(s) |
halic@genzentrum.lmu.de
|
| Organization name |
Ludwig-Maximilians-Universität
|
| Department |
Biochemistry - Gene Center
|
| Lab |
Halic
|
| Street address |
Feodor-Lynen-Str.25
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22681 |
| Series (1) |
| GSE94129 |
Accumulation of RNA on chromatin disrupts heterochromatic silencing |
|
| Relations |
| BioSample |
SAMN06275896 |
| SRA |
SRX2522271 |
