|
| Status |
Public on Feb 09, 2017 |
| Title |
BAA_infected3 |
| Sample type |
SRA |
| |
|
| Source name |
BAA_infected
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Caco-2
treatment: C. concisus BAA infection
|
| Treatment protocol |
Infection with C. concisus BAA
|
| Growth protocol |
Caco-2 cells were grown in Minimal Essential Media, supplemented with 10% v/v Fetal Bovine Serum, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 2.25 mg l-1 sodium bicarbonate and 100 μg ml-1 penicillin and streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the Isolate II RNA Extraction Mini Kit (Bioline)
Illumina TruSeq RNA Sample Prep Kit (version 3) according to manufacturer's instructions, with 2 µg of total RNA being used per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
DynamicTrim.pl + LengthSort.pl
Mapped trimmed read to hg19 using tophat/2.0.4
Used htseq-count to get count values for individual samples
Genome_build: hg19
Supplementary_files_format_and_content: Combined counts file.
|
| |
|
| Submission date |
Jul 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Nandan P Deshpande |
| E-mail(s) |
n.deshpande@unsw.edu.au
|
| Organization name |
Systems Biology Initiative
|
| Department |
School of Biotechnology and Biological Sciences
|
| Street address |
Kensington Campus
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
20 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE84335 |
Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells [BAA] |
| GSE84338 |
Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells |
|
| Relations |
| BioSample |
SAMN05384850 |
| SRA |
SRX1940957 |
