|
| Status |
Public on Apr 07, 2024 |
| Title |
IMPRINT1_S433 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Escherichia coli |
| Characteristics |
cell line: bacteria
strain: EC135
treatment: Amplified in liquid culture
biological replicate: NA
|
| Treatment protocol |
Bifidobacterium breve was resuspend in 250uL of 30mg/mL lysozyme and incubate at 37°C for 30 minutes at 250 rpm, then removed lysozyme mix to harvest cells.
|
| Growth protocol |
Escherichia coli was grown in LB media supplemented with 100 µg/mL ampicillin; Bifidobacterium breve was grown on reinforced clostridial agar with 20 ug/mL tetracycline or in MRS liquid broth (BD CN# 288130) supplemented with 0.03% L-cysteine and 20 ug/mL tetracycline.
|
| Extracted molecule |
other |
| Extraction protocol |
Zyppy Plasmid Miniprep Kit
A plasmid library containing a stretch of nine randomized nucleotides was used. For NGS library preparation, adapters and unique dual indices based on Illumina TruSeq were added in a two-step amplification process using the KAPA HiFi HotStart Library Amplification Kit (KAPA Biosystems, KK2611), according to manufacturer's protocols. The samples were purified with Agencourt AMPure XP (Beckman Coulter, A63881).
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end reads were merged using BBMerge (version 38.69) with parameters “qtrim2=t, ecco, trimq=20, -Xmx1g”
Sequences with perfect matches of flanking sequences were extracted as potential RBS regions using a Python script
After filtering by 10 count per million in minimal 2 samples, differential abundance (log2FC) of potential RBS region sequences between time points was calculated using the quasi-likelihood F test after fitting in a generalized linear model.
Supplementary files format and content: TSV, counts of each RBS sequence in different samples
Supplementary files format and content: CSV, normalized differential abundance of each RBS sequence in different samples
Library strategy: DNA-seq
|
| |
|
| Submission date |
Aug 11, 2023 |
| Last update date |
Apr 08, 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 |
GPL25368 |
| Series (1) |
| GSE240651 |
A cell-free pipeline for recreating methylation patterns radically enhances DNA transformation in bacteria |
|
| Relations |
| BioSample |
SAMN36946853 |
| SRA |
SRX21337804 |
