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Sample GSM425316 Query DataSets for GSM425316
Status Public on Jun 26, 2010
Title NSC-520g-exp2-dff-2
Sample type RNA
 
Source name PNET cell line, miR-520g
Organism Homo sapiens
Characteristics cell line: PNET
cell type: neural stem cell
miRNA: miR-520g
Extracted molecule total RNA
Extraction protocol Standard Trizol extraction.
Label biotin
Label protocol Following manufacturer's instructions, 250 ng total RNA was used for cRNA in vitro transcription and labeling with the Illumina TotalPrep RNA Amplication Kit using biotinylated-UTP (Ambion, Austin, TX).
 
Hybridization protocol Hybridization is carried out in Illumina Intellihyb chambers at 58 °C (Whole-Genome Gene Expression with IntelliHyb Seal System Manual, 2006, Illumina).
Scan protocol Following hybridization, washing, and staining with streptavidin-Cy3, the chips were scanned using an Illumina BeadArray reader.
Description Experiment 2
Replicate 2
(d) 520g-r2
Data processing Data analyses were performed with Illumina BeadStudio (v3.4.0) and Bioconductor packages (v2.3) in the R programming environment (v 2.7.1). The image data were analyzed using the BeadStudio, the output files of which were imported into the R using the lumi package (v1.8.3). Probe set signal intensities were averaged. Expression profiles were then log2 transformed and quantile normalized for ownstream analyses.
 
Submission date Dec 07, 2010
Last update date Dec 07, 2010
Contact name David J. H. Shih
E-mail(s) david.shih@utoronto.ca
Phone (416) 813-7654
Organization name Hospital for Sick Children
Department Developmental and Stem Cell Biology
Lab Peter Gilgan Centre for Research and Learning
Street address 686 Bay St
City Toronto
State/province ON
ZIP/Postal code M5G 0A4
Country Canada
 
Platform ID GPL6947
Series (1)
GSE16988 Expression profile of cell lines overexpressing miR-520g

Data table header descriptions
ID_REF
VALUE Averaged, log2-transformed, and quantile-normalized gene expression values

Data table
ID_REF VALUE
ILMN_1762337 6.287649168
ILMN_1736007 6.608190432
ILMN_2383229 6.271085342
ILMN_1671474 6.533448009
ILMN_1772582 6.260775499
ILMN_1735698 6.370053315
ILMN_1653355 6.557266045
ILMN_1787689 6.285959129
ILMN_1745607 8.002844515
ILMN_2136495 6.203856123
ILMN_1668111 6.378463016
ILMN_1735045 6.336373319
ILMN_1680754 6.451446365
ILMN_2375184 6.207597272
ILMN_1755321 7.081200116
ILMN_1698554 8.007210664
ILMN_1814092 6.228914844
ILMN_1760414 6.341720382
ILMN_2061446 7.131666611
ILMN_1752884 6.263600431

Total number of rows: 37846

Table truncated, full table size 919 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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