|
| Status |
Public on Mar 07, 2018 |
| Title |
IBD_DSS_NLRX1_RNASEQ_001 |
| Sample type |
SRA |
| |
|
| Source name |
Whole colon
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL6/J
genotype: Wild-type
treatment: Negative control
length of treatment: 0min
|
| Treatment protocol |
After mice were euthanized, colons were excised, scored and washed 3 times in phosphate buffered saline solution. Tissue was homogenized and processed using and RNAeasy MiniKit.
|
| Growth protocol |
Induction of colitis protocol: C57BL/6 wild-type (WT) and NLRX1-/- mice ranging from 6-8 weeks of age were administered 8% high molecular weight DSS (average 500,000 molecular weight, Fisher Scientific) in drinking water for seven days. Control mice received normal water. Mice were housed in laboratory animal facilities at the Virginia Tech in a room maintained at 22°C, with a 12-h-light/-dark cycle and fed standard rodent diet free-choice. On day 7, all mice were euthanized via carbon dioxide narcosis with secondary bilateral thoracotomy. All mice were weighed and scored daily. Clinical scores were based physical appearance (0-3), fecal consistency (0-3), presence of rectal bleeding (0-4), and weight loss (0-3) and assigned a compounded score for overall disease activity. All experimental procedures were approved by the Institutional Animal Care and Use Committee of the Virginia Tech.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
IBD_DSS_NLRX1_02_011
|
| Data processing |
Adapter trimming
Bowtie was used to map the reads to RefSeq sequences of mouse (downloaded from UCSC), and RSEM was used to calculate expression values for each gene. FPKM-transformed values were log-transformed followed by normal quantile transformation. Two methods of P-value adjustment (FDR & Bonferroni) were used. Kolmogorov-Smirnov test was used to test normality, followed by parametric 3-way ANOVA to obtain differential expression.
Genome_build: mm9
|
| |
|
| Submission date |
Apr 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Monica Viladomiu |
| E-mail(s) |
monica@vt.edu
|
| Organization name |
Nutritional Immunology and Molecular Medicine Laboratory
|
| Department |
Virginia Bioinformatics Institute
|
| Street address |
1015 Life Science Circle
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE68419 |
Global transcriptomic analysis of colons of wild type and NLRX1-/- mice with IBD |
|
| Relations |
| BioSample |
SAMN03573837 |
| SRA |
SRX1014131 |
