|
| Status |
Public on Jul 08, 2021 |
| Title |
SP-D_1 |
| Sample type |
SRA |
| |
|
| Source name |
in vitro culture (AKI medium)
|
| Organism |
Vibrio cholerae H1 |
| Characteristics |
culture type: in vitro
condition: SP-D
|
| Treatment protocol |
SP-D and denatured SP-D.
|
| Growth protocol |
in vitro culture in AKI medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were harvested and preserved using Trizol reagent. Total RNA was extracted using the RNeasy mini kit (Qiagen).
Migs center.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Functional protein
|
| Data processing |
Reads were trimmed using Trim Galore with automatic adapter sequence detection.
Trimmed reads were mapped to the V. cholerae reference genome and annotation using RNA STAR.
Feature Counts was used to build a count matrix from mapped reads using the Ensembl annotation as a guide.
Genome_build: V. cholerae KW3 genome (NZ_CP006947.1, NZ_CP006948.1).
Supplementary_files_format_and_content: FeatureCounts.txt: Tab-delimited text file
Supplementary_files_format_and_content: SPD_Denatured_FinalAnalysisDESeq2.csv: Comma-separated txt file
|
| |
|
| Submission date |
Jul 06, 2021 |
| Last update date |
Sep 25, 2021 |
| Contact name |
Matthew K Waldor |
| Organization name |
Harvard Medical School
|
| Department |
Microbiology
|
| Lab |
Waldor Lab
|
| Street address |
181 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL30356 |
| Series (2) |
| GSE179529 |
Proteomic analysis of the pathogen surface in cholera identifies host proteins involved in defense and microbiota recognition [II] |
| GSE179530 |
Proteomic analysis of the pathogen surface in cholera identifies host proteins involved in defense and microbiota recognition |
|
| Relations |
| BioSample |
SAMN20080090 |
| SRA |
SRX11360090 |
