|
| Status |
Public on Mar 23, 2018 |
| Title |
tR(CCU)J_23C |
| Sample type |
SRA |
| |
|
| Source name |
cell culture
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
generation: 14.9
environment: 23°C in YPD
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Gentra Puregene Yeast/Bact. Kit
PCR amplification using KAPA HiFi HotStart DNA Polymerase to add adaptors
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
5 replicates of amplicon sequencing
|
| Data processing |
Only perfectly matched fully overlapping paired-end reads were used in estimating genotype frequencies.
The change in relative genotype frequency during the competition was used to estimate the fitness of each genotype relative to the wild-type.
The fitness of a genotype is calculated by averaging the fitness among biological replicates.
We focused on 23,284 genotypes with read counts ≥ 100 before the competition.
Supplementary_files_format_and_content: Fitness for 23284 variant across 4 environments
|
| |
|
| Submission date |
Mar 07, 2018 |
| Last update date |
Mar 23, 2018 |
| Contact name |
Chuan Li |
| E-mail(s) |
chuanli@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Biology
|
| Lab |
Dmitri Petrov lab
|
| Street address |
327 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE111508 |
Multi-environment fitness landscapes of a tRNA gene |
|
| Relations |
| BioSample |
SAMN08644599 |
| SRA |
SRX3770774 |
