|
Status |
Public on Jan 31, 2024 |
Title |
FACS gate B rep 3 bio rep 1 |
Sample type |
SRA |
|
|
Source name |
HEK293T
|
Organism |
synthetic construct |
Characteristics |
cell line: HEK293T
|
Extracted molecule |
genomic DNA |
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
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|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
vamp_parkin.csv
|
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 |
GPL19424 |
Series (1) |
|
Relations |
BioSample |
SAMN39676752 |
SRA |
SRX23454081 |