|
| Status |
Public on Jun 18, 2024 |
| Title |
BL21, Arabinose (A), Replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
BL21 (DE3)strain
|
| Organism |
Escherichia coli |
| Characteristics |
cell type: BL21 (DE3)strain
genotype: E. coliB F- ompT gal
treatment: Arabinose
|
| Treatment protocol |
0.05% arabinose or 2% Glucose were supplmented with liquid medium or added in agar plates
|
| Growth protocol |
E.coli BL21 cells were maintained in lysogeny broth (LB) medium, CA244 strain were grown in LB and M9 minum medium
|
| Extracted molecule |
other |
| Extraction protocol |
Plasmids were isolated from treated or control samples with Roche High Pure Plasmid Isolation Kit
peptide-coding genes were PCR-amplified from isolated plasmids with Q5 DNA polymerase (New England Biolabs)
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Amplicon Sequencing
NS_aa_table_filtered_raw_counts.txt
|
| Data processing |
The raw reads were trimmed to the size of the peptide gene and those containing internal ambiguous bases or being less than 60 bases in length were discarded. The nucleotide sequences were translated into amino acid sequences and the peptides lacking N-terminal methionine or deviating from the size of the expected sequence were eliminated.
Peptides with less than 100 reads in each of the pApi(Glu) samples were also discarded.
Subsequently, the filtered data underwent differential abundance analysis using the standard workflow of edgeR within the R/Bioconductor package
For Positive selection, raw data was processed with Geneious Prime software (v. 2022.2)
Assembly: Api Ib peptide
Supplementary files format and content: For neagtive selection, tab-delimited text file includes raw counts for each sample
Supplementary files format and content: For Positive selection, spreadsheet include raw counts
Library strategy: Amplicon Sequencing
|
| |
|
| Submission date |
Jun 14, 2024 |
| Last update date |
Jun 18, 2024 |
| Contact name |
Alexander Mankin |
| E-mail(s) |
shura@uic.edu
|
| Organization name |
University of Illinois at Chicago
|
| Department |
College of Pharmacy
|
| Lab |
Mankin/Vázquez-Laslop lab
|
| Street address |
900 S. Ashland Ave, Rm. 3052,
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60612 |
| Country |
USA |
| |
|
| Platform ID |
GPL16085 |
| Series (1) |
| GSE269894 |
Sequence diversity of apidaecin-like peptides arresting the terminating ribosome |
|
| Relations |
| BioSample |
SAMN41842437 |
| SRA |
SRX24932301 |
