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Sample GSM7100763 Query DataSets for GSM7100763
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

Supplementary file Size Download File type/resource
GSM7100763_1012-2.counts.txt.gz 770.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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