|
| Status |
Public on May 22, 2023 |
| Title |
select_wt_replicate2_tile3 (45) |
| Sample type |
SRA |
| |
|
| Source name |
Yeast cells
|
| Organism |
synthetic construct |
| Characteristics |
yeast strain: BY4741
selection: yes
molecule subtype: plasmid
|
| Growth protocol |
Following library transformations, yeast cells were expanded in SC-URA medium until saturation. Then, cells for the nonselect condition were harvested and stored at -20C prior to plasmid DNA extraction. In addition, yeast cells were washed and grown on solid SC+leucine+methionine+histidine medium with 100 µg/mL methotrexate and 1 mM sulfanilamide at 37C for four days. Following selection, the cells were harvested and stored at -20C prior to plasmid DNA extraction.
|
| Extracted molecule |
other |
| Extraction protocol |
For all conditions, plasmid DNA was extracted from 9 OD units of yeast cells using the ChargeSwitch Plasmid Yeast Mini kit (Invitrogen).
The Gateway entry libraries were previously constructed (Gersing et al., 2022, bioRxiv) and were cloned into the pDEST-DHFR-PCA Gateway destination vector.
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Amino acid positions 70-103
|
| Data processing |
Libraries were sequenced on a NextSeq 550 instrument (Illumina) and base called using the instrument's Real Time Analysis software.
Sequencing reads were converted to fastq format and demultiplexed using BaseSpace Sequence Hub.
Reads were aligned and variants called using the TileSeq mutation count pipeline (https://github.com/RyogaLi/tileseq_mutcount) version 0.5.9
Variant calls from the TileSeq mutation count pipeline were then used for calling protein-level amino acid changes and for calculating the enrichment of variants using the TileSeqMave pipeline (https://github.com/jweile/tileseqMave) version 1.1.0
Reference sequence: sequence.txt on the Series record contains the sequence used for read alignment.
Library strategy: Tile-Seq
|
| |
|
| Submission date |
Mar 06, 2023 |
| Last update date |
May 22, 2023 |
| Contact name |
Sarah Gersing |
| E-mail(s) |
sarah.gersing@bio.ku.dk
|
| Organization name |
University of Copenhagen
|
| Street address |
Ole Maaløes vej 5
|
| City |
Copenhagen N |
| State/province |
- |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL27609 |
| Series (1) |
| GSE226732 |
Characterizing glucokinase variant mechanisms using a multiplexed abundance assay |
|
| Relations |
| BioSample |
SAMN33602867 |
| SRA |
SRX19576683 |
