|
| Status |
Public on Feb 15, 2013 |
| Title |
L3 |
| Sample type |
SRA |
| |
|
| Source name |
C. jejuni-resistant_no colonization
|
| Organism |
Gallus gallus |
| Characteristics |
breed: Barred Rock chickens
c. jejuni-susceptibility: resistant
caecal colonization level: nil-colonized
tissue: whole caecum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol using the Qiagen RNeasy Lipid purification kit
Libraries were prepared according to instruction in the Illumina protocol Part # 1004898 Rev. A September 2008. Poly-A mRNA was first isolated from total RNA using oligodT beads. The mRNA was then fragmented using divalent cations at 94°C. mRNA was converted to cDNA, blunt-ended at both ends using T4 DNA polymerase and Klenow DNA polymerase. A single A base was then added to the 3′ end to prepare for ligation to adapter sequence. cDNA templates were then size-selected by visualization and excision from agarose gel and purified. The resulting cDNA fragments were PCR-amplified and sequenced generating 40-bp reads using the Illumina Genome Analyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Reads were clipped by 4 bp at the 3' end and aligned with bowtie v0.10.1, allowing 3 mismatches per read.
The number of counts falling on each gene model was determined with Erange v3.3.
Genome_build: Gallus_gallus-2.1 at http://www.ncbi.nlm.nih.gov/assembly/GCF_000002315.2/
Supplementary_files_format_and_content: Tab-separated text file of raw counts per gene for each individual
|
| |
|
| Submission date |
Feb 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Sarah Connell |
| E-mail(s) |
saconnel@tcd.ie
|
| Organization name |
Trinity College Dublin
|
| Street address |
College Green
|
| City |
Dublin |
| ZIP/Postal code |
2 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL9385 |
| Series (1) |
| GSE44341 |
Avian resistance to Campylobacter jejuni colonization is associated with an intestinal immunogene expression signature identified by mRNA sequencing. |
|
| Relations |
| SRA |
SRX237463 |
| BioSample |
SAMN01921064 |
