|
| Status |
Public on Jan 31, 2024 |
| Title |
Barcode-variant plasmid part 2 |
| 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) |
|
| Relations |
| BioSample |
SAMN39676712 |
| SRA |
SRX23454121 |
