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Sample GSM1155636 Query DataSets for GSM1155636
Status Public on Feb 12, 2014
Title Mouse 1, 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 784
7991003006_A
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

Data table header descriptions
ID_REF
VALUE quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 1095.73 0.00
ILMN_2721178 353.55 0.00
ILMN_3033922 558.78 0.00
ILMN_3092673 2052.78 0.00
ILMN_2816356 110.58 0.01
ILMN_2808939 636.38 0.00
ILMN_2634564 278.80 0.00
ILMN_2737647 93.27 0.65
ILMN_2734484 204.13 0.00
ILMN_2952292 132.68 0.00
ILMN_2699078 95.60 0.39
ILMN_1213681 198.75 0.00
ILMN_2735413 110.15 0.01
ILMN_2735415 108.93 0.01
ILMN_2891688 365.92 0.00
ILMN_2637698 554.37 0.00
ILMN_2674228 216.59 0.00
ILMN_2601546 99.67 0.13
ILMN_1230831 97.35 0.24
ILMN_2848071 100.50 0.10

Total number of rows: 25697

Table truncated, full table size 618 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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