|
| Status |
Public on Mar 01, 2015 |
| Title |
RITS-associated small RNAs |
| Sample type |
SRA |
| |
|
| Source name |
tas3-TAP 3xFLAG-ago1 haploid cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: SPY2556
genotype: h+ leu1-32 ade6-M216 ura4-D18 imr1R(NcoI)::ura4+ tas3-TAP-kanMX6 hphMX6-3xFLAG-ago1
|
| Growth protocol |
Cells were grown in rich media (YES)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from Tas3-TAP, TAP-Arb1 or 3xFLAG-Ago1 affinity purifications. Small RNAs were size-selected (18-28 nt) by polyacrylamide gel electrophoresis.
Library construction was conducted as described (Halic and Moazed, 2010, PMID 20178743). Small RNAs were ligated to a 3’ adaptor. The ligated species were size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 5’ adaptor. RNA was then reverse transcribed into cDNA and PCR-amplified in a two-step process. Amplified cDNA was gel-purified and sequenced on the indicated Illumina platform.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Immunoprecipitated and size-selected RNA
|
| Data processing |
Base-calling was performed using CASAVA-1.8.2
Reads lacking the first 5 nt of the linker sequence (CTGTA), containing fewer than 17 nt before the CTGTA, or 10 or more consecutive A bases were removed.
Remaining reads were aligned to the Schizosccharomyces pombe genome using NovoAlign (http://www.novocraft.com/), with configurations -r random -s 1.
Reads aligning with more than one mismatch were removed and all remaining aligned reads were included in all further analyses.
These remaining reads were converted to an Integrated Genome Viewer (IGV)-viewable format.
Genome_build: ASM294v1, S. pombe h- (GCA_000002945.1)
Supplementary_files_format_and_content: IGV-viewable files are tab-delimited and include reads per million at each nucleotide position.
|
| |
|
| Submission date |
Jan 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Holoch |
| E-mail(s) |
daniel.holoch@curie.fr
|
| Phone |
0156246553
|
| Organization name |
Institut Curie, Centre de Recherche
|
| Department |
Genetics and Developmental Biology Unit
|
| Lab |
Raphaël Margueron
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| State/province |
Cedex 05 |
| ZIP/Postal code |
75248 |
| Country |
France |
| |
|
| Platform ID |
GPL15167 |
| Series (1) |
| GSE65223 |
Small RNA loading licenses Argonaute for assembly into a transcriptional silencing complex |
|
| Relations |
| BioSample |
SAMN03292265 |
| SRA |
SRX850956 |
