|
| Status |
Public on Sep 10, 2009 |
| Title |
smallRNA-S.castellii-ago1KO |
| Sample type |
SRA |
| |
|
| Source name |
log-phase liquid culture, ∆ago1
|
| Organism |
Naumovozyma castellii |
| Characteristics |
strain: DPB002
|
| Growth protocol |
Liquid cultures were grown at 25ºC (S. castellii and K. polysporus) or 30ºC (S. bayanus, S. cerevisiae and C. albicans) to log-phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using hot phenol from log-phase YPD cultures. Small-RNA cDNA libraries were prepared as described in Grimson et al. (2008).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Small RNA sequencing, 18-30 nt size selection.
|
| Data processing |
After removing the adaptor sequences, reads representing the small RNAs were collapsed to a non-redundant set, and 14–30-nt sequences were mapped to the appropriate genome, allowing no mismatches and recovering all hits. The processed files are collapsed to unique sequences (1 line per sequence); the second (numeric) value in each column is the number of times each unique sequence was sequenced.
|
| |
|
| Submission date |
Sep 01, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
David Eric Weinberg |
| E-mail(s) |
david.weinberg@ucsf.edu
|
| Phone |
415-514-9723
|
| Organization name |
University of California, San Francisco
|
| Lab |
Weinberg
|
| Street address |
600 16th Street, GH S572F
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL15027 |
| Series (2) |
|
| Relations |
| SRA |
SRX012935 |
| BioSample |
SAMN00005078 |
