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Sample GSM1441398 Query DataSets for GSM1441398
Status Public on Jul 23, 2014
Title Con [9253995035_G]
Sample type RNA
 
Source name Con
Organism Mus musculus
Characteristics strain: C57Black6
gender: male
tissue: intestinal organoids
exposed to: standard organoid culturing medium
Extracted molecule total RNA
Extraction protocol Cultured organoids were pooled, approximately 300 individual organoids per sample, and RNA was isolated using Trizol (Invitrogen, Breda, the Netherlands), followed by purification using the RNeasy Kit (Qiagen). Samples were assayed for quantity and quality with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and NanoDrop Spectrophotometer (NanoDrop, Wilmington, DE).
Label biotin
Label protocol Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX, U.S.A.) according to the manufacturer’s specifications with an input of 200 ng total RNA.
 
Hybridization protocol Total mRNA was amplified, biotinylated and randomly hybridized to MouseRef-8 v2 Expression bead arrays (Illumina, Inc., San Diego, CA, U.S.A.) following standard Illumina hybridization protocol.
Scan protocol Scanning was performed on the Illumina iScan (Illumina, Inc., San Diego, CA, U.S.A.).
Description 9253995035_G
Data processing Data were extracted using GenomeStudio. Quality control and normalization of microarray data was performed in ArrayAnalyzer (www.arrayanalyzer.org). Non-expressed genes were removed by filtering on detection value (p value ≥0.99 in at least one sample). This resulted in gene expression values for 25,697 probes. For differential expression analysis Limma software was used. Subsequently, expression data of the transcriptomics were log-transformed (base 2). Probes were used for biological interpretation if the p value threshold of <0.01 was passed and if the fold change between two conditions was |1.5|.
 
Submission date Jul 22, 2014
Last update date Jul 23, 2014
Contact name Guus Roeselers
Organization name TNO
Department Microbiology & Systems Biology
Street address Utrechtseweg 48
City Zeist
ZIP/Postal code 3704 HE
Country Netherlands
 
Platform ID GPL6885
Series (1)
GSE59644 Insights into microbial modulation of host peripheral lipid and glucose metabolism using mouse gut organoids

Data table header descriptions
ID_REF
VALUE quantile normalized

Data table
ID_REF VALUE
ILMN_2896528 11.38617958
ILMN_2721178 9.224770274
ILMN_3033922 9.665067774
ILMN_3092673 12.11518703
ILMN_2816356 5.76529764
ILMN_2808939 11.22307291
ILMN_2634564 8.227640047
ILMN_2737647 5.578213847
ILMN_2734484 9.848046172
ILMN_2952292 6.901870642
ILMN_2699078 4.449884728
ILMN_1213681 8.370287456
ILMN_2735413 5.013795705
ILMN_2735415 5.885546132
ILMN_2891688 10.26292855
ILMN_2637698 10.23106592
ILMN_2674228 8.685268217
ILMN_2601546 5.788953494
ILMN_1230831 5.139631991
ILMN_2848071 6.25021683

Total number of rows: 25697

Table truncated, full table size 624 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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