|
Status |
Public on Feb 09, 2017 |
Title |
BAA_untreated1 |
Sample type |
SRA |
|
|
Source name |
BAA_untreated
|
Organism |
Homo sapiens |
Characteristics |
cell line: Caco-2 treatment: control
|
Treatment protocol |
control
|
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 |
SAMN05384851 |
SRA |
SRX1940958 |