|
Status |
Public on Apr 30, 2023 |
Title |
1012-2 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 |
SAMN33773572 |
SRA |
SRX19686282 |