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| Status |
Public on May 03, 2024 |
| Title |
4hpi, pBOMB, UnInduced, rep1 |
| Sample type |
SRA |
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| Source name |
HeLa
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| Organism |
Chlamydia trachomatis |
| Characteristics |
cell line: HeLa
cell type: Epithelial cells
genotype: L2 434/Bu
treatment: Transformed with pBOMB4
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| Growth protocol |
DMEM, 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
C. trachomatis infected HeLa were resuspended in TRIzol (300 ul/ well in 24 well plate). After centrifugation, the aqueous layer containing the total RNA was loaded on the Qiagen column and supplier instructions were followed hereafter. RNA was DNase treated on the column and eluted in MQ water. After RNA extraction, the samples were analyzed by Qubit to check for any degradation of the RNA. The yield of the RNA samples was measured on a Qubit.
RNASeq library prepared using Zymo-seq RiboFree Total RNA Library Kit by Zymo Research, with 10ng of total RNA
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
4 hours infection
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| Data processing |
The intensities of the spots on the images and the base calls are computed directly during the run using Illumina’s Real Time Analysis (RTA) software installed on a computer located in the UCI-GHTF.
Reads were mapped to C. trachomatis L2 434/Bu genome and reads were counted for annotated genes on Qiagen CLC Genomics Workbench (version 21.0.5) software with high stringency settings (mismatch cost 2, and insertion and deletion cost 3, length and similarity fraction 0.8 each, maximum number of hits for a read to 10, and minimum read count fusion table to 5).
Assembly: GCA_000068585.1
Supplementary files format and content: Each processed data file corresponding to the libraries is an Excel (.xlsx) file containing name of C. trachomatis genes, chromosome, region, expression value, TPM value, RPKM value, gene length, unique gene reads, and total gene reads
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| Submission date |
May 06, 2022 |
| Last update date |
May 03, 2024 |
| Contact name |
Syed Meraj Azhar Rizvi |
| E-mail(s) |
syedmerr@uci.edu
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| Organization name |
University of California Irvine
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| Department |
Microbiology and Molecular Genetics
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| Lab |
B210
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| Street address |
University of California Irvine
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| City |
Irvine |
| ZIP/Postal code |
92617 |
| Country |
India |
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| Platform ID |
GPL32238 |
| Series (1) |
| GSE202414 |
Euo is a developmental regulator that represses late genes and activates midcycle genes in C. trachomatis |
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| Relations |
| BioSample |
SAMN28119895 |
| SRA |
SRX15196646 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6122119_4_pBOMB_rep1.xlsx |
68.5 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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