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Sample GSM8047270 Query DataSets for GSM8047270
Status Public on Jan 31, 2024
Title Barcode-variant plasmid part 1
Sample type SRA
 
Source name None
Organism synthetic construct
Characteristics cell line: None
Extracted molecule other
Extraction protocol Genomic DNA was extracted from cells using the DNeasy blood & tissue Kit (Qiagen) following the manufacturer’s protocol titled “Protocol: Purification of Total DNA from Animal Blood or Cells (Spin-Column Protocol)”
A site-saturation library of codon optimized human parkin were custom synthesized and barcoded. Constructs of PRKN 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
A variant-barcode map was made from long-read sequencing of the plasmid before transfection. Reads were aligned to the synthetic barcode-gfp-parkin construct using BWA software
Assembly: NA
Supplementary files format and content: vamp_parkin.csv: Colon separated file format contaning abundance 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 Maaløes Vej 5
City Copenhagen
ZIP/Postal code 2200
Country Denmark
 
Platform ID GPL33815
Series (1)
GSE254618 A mutational atlas for Parkin
Relations
BioSample SAMN39676713
SRA SRX23454120

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

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