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Sample GSM8047577 Query DataSets for GSM8047577
Status Public on Jan 31, 2024
Title Barcode-variant plasmid
Sample type SRA
 
Source name None
Organism synthetic construct
Characteristics cell line: None
Extracted molecule other
Extraction protocol Genomic DNA extraction was performed using Qiagen DNeasy blood & tissue kit (Cat. No. 69506)
A site-saturation library of codon optimized human ASPA were custom synthesized and barcoded. Constructs of ASPA variants fused to GFP and an IRES-mCherry expression control were integrated into a HEK293T landing pad cell line
 
Library strategy OTHER
Library source other
Library selection other
Instrument model Sequel II
 
Description barcode_map.csv.gz
Data processing Barcodes of 18 bases were mapped to variants using exact match.
Normalized populations per FACS gate were used to calculate a protein stability index (PSI) and that was finally normalized to an abundance score where 1 is wildtype and 0 the median PSI of nonsence variants
Toxicity scores were calculated as the slope estimated by a linear regression of the variant frequency at each time point normalized to wildtype
A variant-barcode map was made from long-read sequencing of the plasmid before transfection. Reads were aligned to the synthetic barcode-gfp-ASPA construct using BWA software
Assembly: NA
Supplementary files format and content: abundance_aspa.csv and toxicity_aspa.csv: Colon separated file format contaning abundance and toxicity scores
Supplementary files format and content: barcode_map.csv.gz: Colon separated file format containing the map between barcodes and protein variants
Library strategy: VAMP-seq
 
Submission date Jan 30, 2024
Last update date Jan 31, 2024
Contact name Kristoffer Johansson
Organization name University of Copenhagen
Department Biology
Street address Ole Maal√łes Vej 5
City Copenhagen
ZIP/Postal code 2200
Country Denmark
 
Platform ID GPL33815
Series (1)
GSE254639 Deep mutational scanning reveals a tight correlation between protein degradation and toxicity of thousands of non-native aspartoacylase protein variants
Relations
BioSample SAMN39677038
SRA SRX23454943

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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