|
| Status |
Public on Jan 19, 2018 |
| Title |
6+3h BPDL_3 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells infected with C. trachomatis L2/434/Bu
|
| Organism |
Chlamydia trachomatis |
| Characteristics |
strain: L2/434/Bu
host cell line: HeLa
treatment: BPDL
total hours post-infection: 9h
hours of treatment: 3h
|
| Treatment protocol |
At 6h p.i., complete growth media (DMEM,2.5 mM L-glutamine,10% FBS) containing 100 micromolar 2,2-Bipyridyl or 2 microliters ethanol vehicle was added to infected cells.
|
| Growth protocol |
Seed Hela cels in T75 cm2 flasks for ~24h. At 75% confluency, Chlamydia trachomatis (multiplicity of infection=2) was added in fresh complete media and and allowed to infect (without centrifugation) for 30 minutes at 37C. Monolayers were washed to remove unattached bacteria, and infection proceeded for 6h.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was collected after 3h treatment in Trizol and processed according to the Ribopure bacteria kit (Ambion). DNased RNA was applied to the MegaClear column (Ambion) to remove small RNAs, followed by two rounds of eukaryotic mRNA and rRNA depletion with the MicrobEnrich kit (Ambion), and 1-2 rounds of prokaryotic rRNA depletion with MicrobExpresss kit (Ambion). RNA was ethanol precipitated, and tested for integrity by RNA fragment analysis.
RNA was fragmented using RNAse III and cDNA was prepared as per the Ion Total RNA-seq Kit V2, and sequenced on an Ion Proton chip
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA
|
| Data processing |
Quality control:Sequenced reads were filtered to remove adapters and polyclonal sequences with Torrent Suite Software version 5.0.5.
Merging: Merged multiple fastq files from multiple sequencing chips of same cDNA libraries
Filtering: .fastq files have already been filtered by Torrent Suite to remove adapters and polyclonal sequences; Excluded reads with less than 30 nt with CLC Genomics Workbench
Alignment: Aligned to Chlamydia trachomatis 434/Bu core genome (AM884176) and plasmid (NZ_CP009926) using CLC parameters (Mismatch=2, Insertion=3, Deletion=3, Length=0.8, Similarity=0.8, Global=No, Strand=both, Max hits=10, Expression value=Unique counts, EM estimation=Yes)
Normalization: Quantile with CLC
Statistical Analysis: EdgeR with CLC
Genome_build: AM884176 + NZ_CP009926
Supplementary_files_format_and_content: Excel file with Normalized expression value (NEV), and raw unique reads and statistical analysis.
|
| |
|
| Submission date |
Nov 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Amanda Jo Brinkworth |
| E-mail(s) |
abrinkworth@vetmed.wsu.edu
|
| Phone |
(509) 335-7871
|
| Organization name |
Washington State University
|
| Department |
School of Molecular Biosciences
|
| Lab |
Rey Carabeo
|
| Street address |
1770 NE Stadium Way
|
| City |
PULLMAN |
| State/province |
WA |
| ZIP/Postal code |
99164 |
| Country |
USA |
| |
|
| Platform ID |
GPL24258 |
| Series (2) |
| GSE106761 |
Transcriptional response of C.trachomatis to early-cycle iron-starvation |
| GSE106763 |
Transcriptional response of C.trachomatis to early-cycle and mid-cycle iron-starvation |
|
| Relations |
| BioSample |
SAMN08007739 |
| SRA |
SRX3381856 |
