|
| Status |
Public on Apr 30, 2023 |
| Title |
1021-3 sensitive clinical isolate |
| Sample type |
SRA |
| |
|
| Source name |
protozoan
|
| Organism |
Trichomonas vaginalis |
| Characteristics |
sample type: sensitive clinical isolate
cell type: protozoan
|
| Growth protocol |
All T. vaginalis isolates were grown under anaerobic conditions using Diamond’s Trypticase-Yeast-Maltose (TYM) media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA), according to the manufacturer’s instructions.
Pre-made library -- no library preparation performed
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Trichomonas_vaginalis reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: txid5722
Supplementary files format and content: Tab-delimited text files include raw read counts, gene id, chromosome location, gene length, and strand position for each sample
|
| |
|
| Submission date |
Mar 15, 2023 |
| Last update date |
May 01, 2023 |
| Contact name |
Keonte Jamel Graves |
| E-mail(s) |
keontegraves@uabmc.edu
|
| Phone |
3343012839
|
| Organization name |
The University of Alabama at Birmingham
|
| Department |
Medicine-Infectious Diseases
|
| Lab |
STD research program
|
| Street address |
1900 University Blvd, THT 230
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL33257 |
| Series (1) |
| GSE227448 |
Identification of Trichomonas vaginalis 5-nitroimidazole resistance targets |
|
| Relations |
| BioSample |
SAMN33773568 |
| SRA |
SRX19686286 |
