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Sample GSM7082765 Query DataSets for GSM7082765
Status Public on May 22, 2023
Title nonselect_library_replicate2_tile4 (74)
Sample type SRA
 
Source name Yeast cells
Organism synthetic construct
Characteristics yeast strain: BY4741
selection: no
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 104-137
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 SAMN33602950
SRA SRX19576611

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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