|
| Status |
Public on Jan 01, 2024 |
| Title |
Outgrowth_Overnight_Nonselective_1_10,000_Dilution [R4-v2] |
| Sample type |
SRA |
| |
|
| Source name |
plasmid DNA
|
| Organism |
Bifidobacterium breve |
| Characteristics |
strain: UCC2003
treatment: plasmid DNA transformed into B. breve UCC2003, 20 mg/L, recoveries grown overnight. 20 mg/L Tetracycline then added to transformation recoveries in 1:10,000 dilution cultures that were grown for 48 hours. Plasmid DNA was then extracted from cultures.
dilution: 1:10,000
molecule subtype: plasmid DNA amplified with PCR
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Barcode portion of plasmid amplified with PCR (268 bp) and purified with column, then submitted for sequencing.
Sequencing adaptor added to amplicons, then high-throughput amplicon sequencing performed by Genewiz.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The count for each barcode in the samples was determined using the command "zgrep -c “CTGCNNNN” *.fastq.gz" where NNNN represents each 4-nt barcode
Genome_build: not applicable
Supplementary_files_format_and_content: count for each barcode in the sample
|
| |
|
| Submission date |
Nov 30, 2021 |
| Last update date |
Apr 09, 2024 |
| Contact name |
Chase Beisel |
| E-mail(s) |
chase.beisel@helmholtz-hiri.de
|
| Organization name |
Helmholtz Institute for RNA-based Infection Research
|
| Street address |
Josef-Schneider-Str. 2 / Bau D15
|
| City |
Wuerzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL31014 |
| Series (1) |
| GSE189864 |
A cell-free pipeline for recreating methylation patterns radically enhances DNA transformation in bacteria |
|
| Relations |
| BioSample |
SAMN23514818 |
| SRA |
SRX13262473 |
