|
| Status |
Public on Apr 21, 2014 |
| Title |
rrp6Δtri1Δ, 3 |
| Sample type |
SRA |
| |
|
| Source name |
rrp6Δtri1Δ
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: rrp6-delta tri1-delta
|
| Growth protocol |
S. pombe cells were grown on rich media (YES).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gel-purified Ago1-associated RNAs were incubated with 2μM pre-adenylated 3’-adaptor oligonucleotide (miRNA Cloning Linker-1 from IDT, AppCTGTAGGCACCATCAAT/ddC/), 1 U/μL RNAsin (Promega), 1 U/μL T4 ligase (Takara) in 10 μL ligation buffer without ATP at 20°C for 2h minutes. The 3´-ligation reaction was purified on a 17% gel. For the 5’-ligation, 3´-ligated products were incubated with 2 pmol 5’ adaptor oligonucleotide (GUU CAG AGU UCU ACA GUC CGA CGA UC), 1 U/μL RNAsin (Promega), 0.06 μg/μL BSA ,1 U/μL T4 ligase (Promega) in 10μL ligation buffer at 20°C for 2 hours. The ligated reaction was gel purified and used for first strand cDNA synthesis with RT oligo (ATT GAT GGT GCC TAC AG) for 1h at 44°C in 1x first strand buffer, 10mM DTT, 0.2 mM dNTP, 1 U/μL RNAsin (Promega) and Superscript III. cDNA was amplified using PCR with Illumina P5 (AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAC GAT C) and Illumina P7 (CAA GCA GAA GAC GGC ATA CGA ATT GAT GGT GCC TAC AG ) oligos for 10-15 cycles and gel purified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
schizosaccharomyces_pombe_972h_20080716
rrp6Dtri1D.igv; rrp6Dtri1D-minus.igv; rrp6Dtri1D-plus.igv;
|
| Data processing |
base calling
sRNA-seq reads were aligned to the pombe genome assembly using Novoalign version 2 with the standard settings
Reads mapping with two or fewer mismatches were retained.
Enrichments were calculated with our house scripts
Genome_build: schizosaccharomyces_pombe_972h_20080716
Supplementary_files_format_and_content: can be viewed with IGV browser
Supplementary_files_format_and_content: http://www.broad.mit.edu/igv
|
| |
|
| Submission date |
Jun 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Mario Halic |
| E-mail(s) |
halic@genzentrum.lmu.de
|
| Organization name |
Gene Center, University of Munich
|
| Department |
Department of Biochemistry
|
| Street address |
Feodor-Lynenstr. 25
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9453 |
| Series (1) |
| GSE38636 |
Argonaute and Trimmer generate Dicer-independent priRNAs and nucleate RNAi |
|
| Relations |
| SRA |
SRX153055 |
| BioSample |
SAMN01047765 |
