|
| Status |
Public on Aug 24, 2014 |
| Title |
Log Phase 1 IVT +CMC |
| Sample type |
SRA |
| |
|
| Source name |
BY4741
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
growth condition: Log phase: OD260 = 0.8
strain: BY4741
treatment: +CMC
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hot phenol chloroform extraction, 2x poly(A) purification with Ambion polyA Purist Kit
PSI-seq. Libraries were constructed as described in Lovejoy et al.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
PSI-seq
|
| Data processing |
Aligned to the S. cerevisiae genome using bowtie-0.12.5. Conditions -p 6 -v 3 -q -a --best --strata
Counted reads stopping at each nucleotide in each sequencing run. Merged these data into one table, then sorted the table to get sorted_genomic_reads.txt
Genome_build: saccer3
|
| |
|
| Submission date |
Aug 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander F Lovejoy |
| Organization name |
Stanford University
|
| Department |
Biochemistry
|
| Lab |
Brown
|
| Street address |
279 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94306 |
| Country |
USA |
| |
|
| Platform ID |
GPL9377 |
| Series (1) |
| GSE60445 |
PSI-seq to Identify Sites of Pseudouridylation in S. cerevisiae |
|
| Relations |
| BioSample |
SAMN02991353 |
| SRA |
SRX681896 |
