|
| Status |
Public on Jan 30, 2024 |
| Title |
50MOI_1hpi_3 |
| Sample type |
SRA |
| |
|
| Source name |
50MOI_1hpi
|
| Organism |
Chlamydia trachomatis |
| Characteristics |
genotype: L2 434/BU
group: 50 MOI
time: 1 hpi
|
| Growth protocol |
L2-infected L929 cells were cultured in DMEM supplemented with 5% fetal bovine serum (FBS) at 37 ℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Tri Reagent (MilliporeSigma). Genomic DNA was removed using RNase-free DNase I-XT (New England Biolab).
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 host and bacterial rRNAs and host mRNAs.
|
| |
|
| 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).
Assembly: Combined genome including Chlamydia trachomatis 434/Bu chromosome (GCF_000068585.1_ASM6858v1), C_trachomatis_pL2_plasmid_AM886278, and mouse genome (mm10).
Supplementary files format and content: tab-delimited text files include raw count values for each sample
|
| |
|
| Submission date |
Nov 29, 2023 |
| Last update date |
Jan 30, 2024 |
| 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) |
| GSE248988 |
Supermajority of Chlamydia trachomatis genes are activated during the first hour of infection |
|
| Relations |
| BioSample |
SAMN38503686 |
| SRA |
SRX22683629 |
