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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
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Library strategy |
OTHER |
Library source |
other |
Library selection |
other |
Instrument model |
Sequel II |
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|
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
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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 Maaløes 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 |