|
| Status |
Public on Apr 11, 2019 |
| Title |
Caco2_2.5_2 |
| Sample type |
SRA |
| |
|
| Source name |
C. jejuni_co-culture with Caco-2 cells
|
| Organism |
Campylobacter jejuni |
| Characteristics |
strain: 81-176
culture time (hours): 2.5
culture condition: Co-culture with Caco-2 cells in MEM + 1% FBS
|
| Growth protocol |
C. jejuni were grown in 250 mL MH broth cultures in a microaerobic environment shaking at 220 rpm on an orbital shaker, adjusted to an OD540 of 0.3 in MEM + 1% FBS, and added to T75 flasks of cultured epithelial cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial pellets were collected by centrifugation and snap frozen. RNA Extraction was done using the Ambion Ribopure Bacteria kit. rRNA was depleted with 3’ biotinylated oligonucleotides that were designed to hybridize with C. jejuni 16S and 23S rRNAs.
Illumina MiSeq libraries were prepared using the KAPA stranded RNAseq kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Enriched mRNA
|
| Data processing |
For files from the Illumina MiSeq instrument, MiSeq Instrument Software was used to generate fastq files. For files generated by the Ion Proton instrment, BaseCaller (Torrent Suite verision 5.0.4) was used for basecalling and demultiplexing.
Reads were aligned to the genome using bowtie2 version 2.3.2 using default options.
Reads mapping to each CDS were counted using featureCounts from the subread package, version 1.5.3 using the --largestOverlap option.
Genome_build: Genbank accession numbers for the sequences used for read mapping are as follows: C. jejuni strain 81-176 [chromosome sequence: (NC_008787), plasmid sequences: pTet (NC_008790) and pVir (NC_008770)];
Supplementary_files_format_and_content: Comma delimited text file containing counts of mapped transcripts CDS for each strain.
|
| |
|
| Submission date |
May 25, 2018 |
| Last update date |
Apr 11, 2019 |
| Contact name |
Michael E Konkel |
| E-mail(s) |
konkel@wsu.edu
|
| Organization name |
Washington State University
|
| Street address |
PO Box 647520
|
| City |
Pullman |
| State/province |
WA |
| ZIP/Postal code |
99164 |
| Country |
USA |
| |
|
| Platform ID |
GPL22824 |
| Series (1) |
| GSE114909 |
Campylobacter jejuni demonstrates conserved proteomic and transcriptomic responses when co-cultured with human INT 407 and Caco-2 epithelial cells |
|
| Relations |
| BioSample |
SAMN09259228 |
| SRA |
SRX4123770 |
