|
| Status |
Public on Oct 31, 2023 |
| Title |
Control 1 |
| Sample type |
SRA |
| |
|
| Source name |
Culture
|
| Organism |
Treponema denticola ATCC 35405 |
| Characteristics |
tissue: Culture
strain: ATCC 35405
treatment: Control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pellet under anaerobic conditions. Resuspend in Qiagen RLT and lyse in MP fast prep. Supernatant prepared with Qiagen Rneasy kit
NEBNext Ultra II Directional RNA kit (#7760) and NEB UDI plate 1 adapters (#6440) using 220 ng input and 11 cycle PCR
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
P1.MET5-4
|
| Data processing |
Downloaded Treponema_denticola_ATCC_35405 GenBank and FASTA files from NCBI. Generated PTT and RNT files using gbkToPttAnd Rnt. Removed genes with incomplete coordinates
Read QC. Assessed raw read quality using FastQC v0.11.7 [2] and MultiQC v1.1 [3]. FastQC revealed adaptor contamination across the libraries. Removed potential adapter contamination using Trimmomatic v0.39; Ran FastQC and MultiQC again to make sure adapters were removed.
Read alignment and counting. Aligned the trimmed reads against the reference using EDGE-Pro v1.3.1. EDGE-Pro also counted reads on each gene included in the PTT and RNT files
Differential expression analysis was performed using DESeq2 v1.32.0 and normalized based on (rlog) expression values
Preliminary, alignment-derived annotations were augmented using the prokaryote-specific BlastX functions of the KEGG genes database (www.genome.jp/tools/blast/) and/or NCBI (blast.ncbi.nlm.nih.gov)
Assembly: NC_002967.9
Supplementary files format and content: tab-delimited text files containing raw gene counts per sample
|
| |
|
| Submission date |
Mar 20, 2023 |
| Last update date |
Oct 31, 2023 |
| Contact name |
David Albert Scott |
| E-mail(s) |
dascot07@louisville.edu
|
| Phone |
5028528905
|
| Organization name |
University of Louisville
|
| Department |
OIID
|
| Lab |
Scott
|
| Street address |
501 S Preston St
|
| City |
Louisville |
| State/province |
KY |
| ZIP/Postal code |
40202 |
| Country |
USA |
| |
|
| Platform ID |
GPL33272 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN33831703 |
| SRA |
SRX19732346 |
