|
| Status |
Public on Dec 26, 2013 |
| Title |
rdp1∆ + vector |
| Sample type |
SRA |
| |
|
| Source name |
rdp1∆ + vector_haploid cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: SPY 2468
genotype/variation: h- ade6-M210 leu1-32 ura4+ rdp1∆::hphMX
transformed with: PDM 829 (vector control)
|
| Growth protocol |
Cells were grown in minimal media lacking leucine (EMMC-LEU)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the hot phenol method (Leeds et al., 1991), and small RNAs were purified using the mirVanaTM miRNA Isolation kit (Ambion). These sRNAs were used for library construction.
Small RNA libraries were constructed as previously described (Halic and Moazed, 2010). Briefly, 20-30nt RNA was size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 3’ adapter. The ligated species were size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 5’ adapter. RNA was then reverse transcribed into cDNA and PCR-amplified in a two-step process. Amplified cDNA was gel-purified and sequenced on Illumina High-Seq 2000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calling was performing using CASAVA-1.8.2
First, reads containing linker sequence and long polyA tracts were removed. Remaining reads were aligned using novoalign (www.novocraft.com) to the S. pombe h- genome, with configurations -l14, -t30, and -r Random.
Reads were then converted to an Integrated Genome Viewer (IGV)-viewable format, mapping the 5' most nucleotide of each small RNA.
Genome_build: 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 |
Nov 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ruby Yu |
| Organization name |
Harvard University
|
| Department |
Cell Biology
|
| Lab |
Danesh Moazed
|
| Street address |
240 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL13988 |
| Series (2) |
| GSE52532 |
Generation of Rdp1-independent primary siRNAs |
| GSE52535 |
Determinants of heterochromatic siRNA biogenesis and function |
|
| Relations |
| BioSample |
SAMN02413289 |
| SRA |
SRX379589 |
