|
Status |
Public on Jan 30, 2024 |
Title |
50MOI_0hpi_1 |
Sample type |
SRA |
|
|
Source name |
50MOI_0hpi
|
Organism |
Chlamydia trachomatis |
Characteristics |
genotype: L2 434/BU group: 50 MOI time: 0 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
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|
|
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 |
SAMN38503691 |
SRA |
SRX22683624 |