|
| Status |
Public on Oct 07, 2020 |
| Title |
Pig WT 6 hour Animal #2 Loop #1 |
| Sample type |
SRA |
| |
|
| Source name |
Pig WT 6 hour Animal #2 Loop #1
|
| Organism |
Campylobacter jejuni |
| Characteristics |
strain/genotype: F38011
culture time (hours): 6
culture condition: Pig ligated intestinal loop
|
| 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 phosphate buffered saline before injection into the intestinal lumen.
|
| Extracted molecule |
polyA 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 |
| |
|
| Data processing |
MiSeq Instrument Software was used to generate fastq files.
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 file associated with accession CP006851.1 was used for mapping reads to the C. jejuni genome.
Supplementary_files_format_and_content: Comma delimited text file containing counts of mapped transcripts CDS.
|
| |
|
| Submission date |
Mar 27, 2020 |
| Last update date |
Oct 07, 2020 |
| 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) |
| GSE147629 |
Development of an in vivo ligated loop model reveals new insight into the host immune response against Campylobacter jejuni |
|
| Relations |
| BioSample |
SAMN14468161 |
| SRA |
SRX8011987 |
