|
| Status |
Public on Jul 08, 2021 |
| Title |
RS7_Euo_NI-2 |
| Sample type |
SRA |
| |
|
| Source name |
Constructed by Wurihan Wurihan
|
| Organism |
Chlamydia trachomatis |
| Characteristics |
strain: L2 Transformed with Euo expression plasmid
protocol: Noninduced
|
| Treatment protocol |
10 nM anhydrotetracycline (IND) or noninduced (NI)
|
| Growth protocol |
L929 monolayers infected with CtL2 transformed with a GrgA, Euo or HrcA expression plasmid, cultured with DMEM supplemented with 5% FBS and 1 µg/ml cycloheximide at 37 °C, 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sigma TRI Reagent
Approximately 1250 – 2000 ng Total RNA was used for RNA-seq library preparation using Illumina TruSeq stranded mRNA-seq sample preparation protocol with the modifications to remove rRNAs from both host and bacteria, and mRNAs from host.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina bcl2fastq software used for base-calling
All RNA-seq Fastq reads were aligned with combined reference genome using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using htseq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Genome_build: Combined genome including Chlamydia trachomatis 434/Bu chromosome (GCF_000068585.1_ASM6858v1), C_trachomatis_pL2_plasmid_AM886278 and mKate gene
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene names and the second column contain the read counts of the gene using htseq-count
|
| |
|
| Submission date |
Jul 02, 2020 |
| Last update date |
Jul 09, 2021 |
| Contact name |
YI ZOU |
| E-mail(s) |
zou@uthscsa.edu
|
| Organization name |
UTHSA-GCCRI
|
| Street address |
8403 Floyd Curl Drive
|
| City |
SAN ANTONIO |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL28812 |
| Series (1) |
| GSE153747 |
A GrgA-Euo-HrcA transcriptional regulatory network controls the growth and development of the obligate intracellular bacterium Chlamydia |
|
| Relations |
| BioSample |
SAMN15434265 |
| SRA |
SRX8659097 |
