|
| Status |
Public on Feb 28, 2023 |
| Title |
wtaav2_virus_biol_rep_2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Adeno-associated virus |
| Characteristics |
cell line: HEK293T
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
NaCl was added to HEK293T cells. Cells were incubated at 37C for 3 hours to lyse. The resulting material was incubated O/N at 4C. The following morning precipitates were removed and discarded. The supernatant was filtered through a 0.2 um PES filter. PEG was added to precipitate viral particles. The following day, viral genome-containing particles were purified by iodixanol gradient ultracentrifugation. Viral genomes were release by incubation of purified viral particles at 98C for 10 minutes prior to barcode amplification for sequencing.
Illumina adapters were added via PCR
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
sequencing of barcoded AAV2 rep variants to determine representation in the viral library
|
| Data processing |
library strategy: amplicon sequencing
Python was used to extract the barcodes from the fastq files and count the occurrence of each barcode in each sample.
Assembly: AAV2
Supplementary files format and content: CSV files containing barcode counts for each sample
|
| |
|
| Submission date |
Feb 27, 2023 |
| Last update date |
Feb 28, 2023 |
| Contact name |
Nina Jain |
| E-mail(s) |
n.kumarijain@gmail.com
|
| Organization name |
Harvard University
|
| Department |
Wyss Institute
|
| Street address |
CLSB 5FL 528/6c, Center for Life Sciences, 3 Blackfan Circle
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL27708 |
| Series (1) |
| GSE226265 |
Comprehensive mutagenesis of AAV2 rep |
|
| Relations |
| BioSample |
SAMN33463106 |
| SRA |
SRX19518339 |
