|
| Status |
Public on Feb 10, 2025 |
| Title |
1h/LB-rep2, SVb3-3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial
|
| Organism |
Vibrio cholerae C6706 |
| Characteristics |
cell type: bacterial
genotype: Wild type
treatment: No treatment/control in LB
|
| Treatment protocol |
Bacterial cultures were diluted to sub-agglutinating conditions of an optical density at 600 nm (O.D.600) of ≤ 0.1 in either LB or LB containing 1% w/v mucin (LBM) and exposed to human monoclonal immunoglobulin (Ig) G1 targeting V. cholerae O-specific polysaccharide component of LPS (clone G1 - CF21.2.G01) and flagellin (clone B12 -AT11.1.B12) for one hour at room temperature
|
| Growth protocol |
Prio to exposure to antibody, V. cholerae El Tor O1 strain C6706 were grown in toxin-inducing-conditions in AKI media (1.5% Bacto-Peptone, 0.4% yeast extract, 0.5% NaCl) supplemented with sodium bicarbonate to a final concentration of 0.3% w/v without agitation at 37 ºC for four hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial cultures were then pelleted, and total RNA was isolated using Lysozyme and RNeasy (Qiagen) per manufacturer’s instructions.
RNA was depleted of ribosomal RNA using a ribosomal depletion kit (NEB) and RNA-seq libraries were constructed using NEBNext Ultra II Directional kit per manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Library name: SVb3-Sample 2
|
| Data processing |
Sequencing reads were mapped to V. cholerae O1 biovar El Tor strain N16961 chromosome I and II separately by using the program Rockhopper.
For differential expression analysis, we used EdgeR, and classified genes as differentially expressed based on the cutoffs of 1.5-fold change in expression value and false discovery rates (FDR) below 0.05.
Assembly: N16961_v2
Supplementary files format and content: text files include raw counts for each sample
|
| |
|
| Submission date |
Jan 24, 2025 |
| Last update date |
Feb 10, 2025 |
| Contact name |
Smriti Verma |
| E-mail(s) |
SVERMA5@mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Department of Infectious Diseases
|
| Lab |
Edward T Ryan Lab
|
| Street address |
55 Fruit Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL35328 |
| Series (1) |
| GSE287993 |
Impact of human anti-O-specific polysaccharide (OSP) antibody on Vibrio cholerae O1 in complex media containing mucin |
|
| Relations |
| BioSample |
SAMN46406787 |
| SRA |
SRX27463352 |
