|
| Status |
Public on Jun 21, 2023 |
| Title |
AB |
| Sample type |
SRA |
| |
|
| Source name |
XL1-Blue
|
| Organism |
Escherichia coli |
| Characteristics |
strain: XL1-Blue
phage: M13 Bacteriophage
phagemid: pMOPAC24
phage display vector: pMopac24 M13 bacteriophage display vector
treatment: A.baumannii bound phage
|
| Extracted molecule |
other |
| Extraction protocol |
Phagemids were prepared from infected E. coli using the Zymo mini prep kit for each dataset. Then using PCR phagemid VHH inserts were amplified using primers that added Illumina adapters and barcodes to th PCR product to be sequenced.
Using PCR phagemid VHH inserts were amplified using primers that added Illumina adapters and barcodes to th PCR product to be sequenced.
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
PE300 V3
|
| Data processing |
Sequence data was assesed for quality of reads
Sequences were counted using Tally
Tallied sequences were filtered for correct and unique VHH translated sequences and the CDR sequences were extracted as well
Translated sequences with more than 1 read were kept for further analysis
A. baumannii binding dataset was filtered by each of the three CDRs (peptide1,2,3) to identify VHHs completely unique to the A. baumannii dataset compared to the control GFP and V. cholerae datasets. See "Filtered A.baumannii Binding VHH.csv" linked to the Series record.
Assembly: NA
Supplementary files format and content: csv of the tallied read counts per VHH identified and the corresponding amino acid sequences for each dataset
Library strategy: Phage Display
|
| |
|
| Submission date |
May 13, 2022 |
| Last update date |
Jun 21, 2023 |
| Contact name |
Bryan Davies |
| E-mail(s) |
bwdavies@austi.utexas.edu
|
| Organization name |
University of Texas at Austin
|
| Street address |
2500 Speedway
|
| City |
Austin |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL16085 |
| Series (1) |
| GSE202972 |
Generation of synthetic Acinetobacter baumannii specific nanobodies |
|
| Relations |
| BioSample |
SAMN28235235 |
| SRA |
SRX15262826 |
