|
| Status |
Public on Apr 01, 2024 |
| Title |
HctB 18hpi sample 3 |
| Sample type |
SRA |
| |
|
| Source name |
Cos-7 cells
|
| Organism |
Chlamydia trachomatis |
| Characteristics |
cell line: Cos-7 cells
treatment: HctB expression at 15 hpi isolated at 18 hpi
|
| Treatment protocol |
Cos-7 Cells were infected with either C. trachomatis L2 434/Bu-clover, L2 434/Bu-euo, L2 434/Bu-hctA, L2 434/Bu-hctB, L2 434/Bu-ctcB
|
| Growth protocol |
Cos-7 cells (CRL-1651) were grown in RPMI-1640, supplemented with 10% FBS and 10 μg/mL gentamicin (Cellgro).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells infected with the indicated strains. Expression of each protein was induced at 15 hpi with either 0.5 mM theophylline and 30ng/ml anhydrotetracycline (HctB) or 0.5 mM theophylline (Clover, HctA, CtcB and Euo) and the Ctr isolated at 18 and 24 hpi on ice. Briefly, the infected monolayer was scraped into ice cold PBS, lysed using a Dounce homogenizer and the Ctr isolated over a 30% MD-76R pad. Total RNA was isolated using TRIzol reagent (Life Technologies) following the protocol provided and genomic DNA removed (TURBO DNA-free Kit, Invitrogen). The enriched RNA samples were quantified and the libraries built and barcoded by the IBEST Genomics Resources Core at the University of Idaho.
Kapa RNA Hyper Prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Aligned with Bowtie2
Counts generated using Htseq
Differentail gene expression calcualted using Dseq2
Assembly: Alinged to C. trachomatis L2 434/Bu using Bowtie2
Supplementary files format and content: Tab delinated text file of counts
|
| |
|
| Submission date |
Mar 27, 2024 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Scott Stephen Grieshaber |
| E-mail(s) |
scottg@uidaho.edu
|
| Phone |
3525750394
|
| Organization name |
University of Idaho
|
| Department |
Biological Sciences
|
| Street address |
875 Perimeter Drive MS 3051
|
| City |
Moscow |
| State/province |
ID |
| ZIP/Postal code |
83844-3051 |
| Country |
USA |
| |
|
| Platform ID |
GPL28812 |
| Series (1) |
| GSE262652 |
Ectopic expression of transcriptional regulatory proteins reveals two classes of late genes during chlamydial development, corresponding to the IB and EB cell type. |
|
| Relations |
| BioSample |
SAMN40633152 |
| SRA |
SRX24087550 |
