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Sample GSM7924314 Query DataSets for GSM7924314
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
 
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

Supplementary file Size Download File type/resource
GSM7924314_F4_Genes_ReadCount.txt.gz 95.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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