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| Status |
Public on Oct 01, 2017 |
| Title |
HI broth + 25mM aspartate microaerophilic log |
| Sample type |
SRA |
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| Source name |
monoculture
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| Organism |
Campylobacter jejuni |
| Characteristics |
strain: 81116
genotype: wild type
treatment: 25mM aspartate
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| Growth protocol |
Campylobacter precultures were diluted to an OD550 of 0.05 and grown microaerophilic (5% O2, 8% CO2, 8% H2) in HI medium, or HI medium + 25mM serine, or HI medium + 25mM aspartate to mid-log phase (6hr) or early stationary phase (12hr).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cultures with the RNA-BeeTM kit (Tel-Test, Inc) according to the manufacturer’s specifications. . Subsequently, RNA was treated with RNAse-free DNAseI (Thermo) according to the instructions of the manufacturer.
Ribozero Magnetic Kit for-gram negative bacteria (Illumina) following manufacturer’s instructions using following the 5ug RNA procedure and option 1 (Ethanol precipitation), except using 1/8th reaction volumes/amounts. Illumina libraries were prepared using the KAPA stranded RNA-seq kit (Kapa Biosystems, Wilmington, MA), following manufacturer’s instructions to produce ~300bp fragments. Standard desalting TruSeq LT primers were ordered from Integrated DNA Technologies (Coralville, IA) and used at 50-100nM final concentration based on starting RNA amount. The PCR step was reduced to 6 cycles. Libraries were quantified using the KAPA Library Quantification Kit (Kapa), except with 10 µl volume and 90 sec annealing/extension PCR. Libraries were pooled and normalized to 4 nM. Pooled libraries were re-quantified by ddPCR on a QX200 system (Bio-Rad), using the Illumina TruSeq ddPCR Library Quantification Kit and following manufacturer’s protocols. The libraries were sequenced in two 2x76bp paired end v3 runs on a MiSeq instrument (Illumina) at 13.5 pM, following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Illumina MiSeq Real-time analysis (RTA) used for basecalling.
Sequenced reads were trimmed for low-quality sequence, then mapped to CP000814 using bowtie v1.1.2 within Geneious v9.1 parameters -n 2 -l 28 -q -p 4 --best --strata
Geneious v9 software was used to calculate the normalized transcripts per million (TPM) and to compare expression levels between the control growth condition (microaerophilic) and experimental conditions (oxygen limited+ nitrate, and oxygen limited).
Genome_build: CP000814.1
Supplementary_files_format_and_content: tab-delimited text files include TKM values for each Sample ...
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| Submission date |
Sep 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Craig T Parker |
| E-mail(s) |
CRAIG.PARKER@ARS.USDA.GOV
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| Phone |
510-559-6187
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| Organization name |
USDA ARS
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| Department |
PSM
|
| Street address |
800 Buchanan St
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| City |
Albany |
| State/province |
CA |
| ZIP/Postal code |
94710 |
| Country |
USA |
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| Platform ID |
GPL22824 |
| Series (1) |
| GSE104231 |
Catabolite repression by intracellular succinate in Campylobacter jejuni |
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| Relations |
| BioSample |
SAMN07695107 |
| SRA |
SRX3215035 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2792948_vanderstel2016-3.csv.gz |
64.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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