|
| Status |
Public on Apr 22, 2021 |
| Title |
Library of viral barcodes |
| Sample type |
SRA |
| |
|
| Source name |
barcodes
|
| Organism |
Suid alphaherpesvirus 1 |
| Characteristics |
strain: SAD B19
modification: G-deficient
|
| Treatment protocol |
B7GG cells were transduced with Rab-delta-G virus.
|
| Growth protocol |
B7GG cells (Osakada et al., Nat Protocols 2013) were grown in B7GG media.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNeasy Kit, reverse transcribed using oligo-dT primers, and amplified with RABID-seq specific primers
Libraries were amplified using RABID-seq specific barcode primers.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Library strategy: Amplicon-seq
The data were demultiplexed using the inDrop pipeline (https://github.com/indrops/indrops) using the library index.
The reads were trimmed using Trimmomatic (v0.39) and the cell barcodes were checked against the cell barcode whitelist provided by the inDrop pipeline.
Reads were trimmed and filtered based on the RABID-seq barcode processing pipeline.
The filtered reads were clustered within 1 Levenshtein distance using Starcode v1.3.
Genome_build: The RABID-seq barcode reads were corrected based on the results from Starcode clustering and counted.
Supplementary_files_format_and_content: Count table for barcode reads
|
| |
|
| Submission date |
May 06, 2020 |
| Last update date |
Apr 22, 2021 |
| Contact name |
Michael Wheeler |
| E-mail(s) |
mwheeler0@bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Neurology
|
| Street address |
60 Fenwood Rd.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL28491 |
| Series (2) |
| GSE149998 |
Analysis of diversity in barcoded virus library |
| GSE150858 |
Barcoded viral tracing of single-cell interactions in CNS inflammation |
|
| Relations |
| BioSample |
SAMN14844539 |
| SRA |
SRX8273520 |
