|
Status |
Public on Feb 12, 2014 |
Title |
Mouse 3, SP |
Sample type |
RNA |
|
|
Source name |
Cecal CD45+ cells
|
Organism |
Mus musculus |
Characteristics |
strain: HBUS tissue: Serrated polyp
|
Extracted molecule |
total RNA |
Extraction protocol |
Intestines were cut into 2 cm pieces and washed in ice-cold PBS. To release the intestinal epithelial cells, the pieces were incubated in PBS containing 1.3 mM EDTA for 30 min at 4°C. After vigorous shaking, intestinal epithelial cells were collected in the supernatant and used to prepare RNA extracts using the RNeasy Mini Kit (QIAGEN). The remaining tissue was digested in DMEM containing 1 mg/ml dispase II (Roche) for 20 min at 37oC, incubated with CD45 microbeads (Miltenyi Biotec) and purified using MACS columns (Miltenyi Biotec) according to manufacture’s protocol. RNA was extracted from the CD45 enriched purified cells using the RNeasy Mini Kit (QIAGEN) including a DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.
|
Label |
biotin
|
Label protocol |
Biotinylated cRNA was prepared from 500 ng total RNA with the Illumina® TotalPrepTM RNA Amplification Kit according to manufactures protocol (AMIL1791) and loaded on MouseRef-8 BeadChip Kit430 2.0 Expression BeadChip arrays.
|
|
|
Hybridization protocol |
Standard Illumina hybridization protocol
|
Scan protocol |
Standard Illumina scanning protocol
|
Description |
790 7991003006_G
|
Data processing |
Raw data files were converted using GenomeStudio and further processed using using lumi v2.10.0 Bioconductor/R and limma v3.14.4 Bioconductor/R.
|
|
|
Submission date |
Jun 07, 2013 |
Last update date |
Feb 12, 2014 |
Contact name |
Gerold Bongers |
E-mail(s) |
gerold.bongers@mssm.edu
|
Organization name |
Icahn School of Medicine at Mount Sinai
|
Department |
Immunology Institute
|
Street address |
1425 Madison Ave, 12-26A
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10029-6574 |
Country |
USA |
|
|
Platform ID |
GPL6885 |
Series (2) |
GSE47734 |
Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice [BeadArray] |
GSE47736 |
Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice |
|