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Sample GSM1486493 Query DataSets for GSM1486493
Status Public on Aug 27, 2014
Title MCF10A exos_1
Sample type RNA
 
Source name breast epithelial cells
Organism Homo sapiens
Characteristics cell/tissue type: normosomes
Treatment protocol Exosomes were extracted from cancer cells and added to the culture media of non-tumorigenic cells.
Growth protocol Cells were grown for RNA as well as for extraction of exosomes for posterior RNA extraction in media with FBS depleted of exosomes.
Extracted molecule total RNA
Extraction protocol Exosomes used for RNA extraction were resuspended in 500ul of Trizol and protocol as detailed by manufacturer. Cells were resuspended in 1000ul of Trizol and protocol as detailed by manufacturer.Cells were grown for RNA as well as for extraction of exosomes for posterior RNA extraction in media with FBS depleted of exosomes.
Label streptavidin-Alexa647 conjugate
Label protocol Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
 
Hybridization protocol The standard Affymetrix hybridization protocol was used - P-AFFY3
Scan protocol Standard Affy scanning protoco - array assay. Quantified using GenePix Pro-6.0.
Description Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).
Data processing The raw intensity for each probe is the median feature pixel intensity with the median background subtracted.  Setting an offset one ensures that there will be no negative values after log-transforming data.  Data was quantile normalized followed by log2 transformation (R computing environment (version 3.0.1)). Signals from probes measuring the same miRNA were averaged. 
 
Submission date Aug 25, 2014
Last update date Aug 27, 2014
Contact name RAGHU KALLURI
Organization name MDACC
Department CANCER BIOLOGY
Street address 1881 East Rd.
City Houston
ZIP/Postal code 77054-1901 TX
Country USA
 
Platform ID GPL19117
Series (2)
GSE60715 Cells and exosomes after cell-free culture
GSE60716 Cell-Independent MicroRNA Biogenesis

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
14q0_st 2.30354732
14qI-1_st 2.422851388
14qI-1_x_st 2.046372769
14qI-2_st 2.319658793
14qI-3_x_st 1.911929578
14qI-4_st 2.075657131
14qI-4_x_st 1.859230312
14qI-5_st 1.777473932
14qI-6_st 1.623163782
14qI-7_st 2.121297418
14qI-8_st 2.319658793
14qI-8_x_st 2.209917887
14qI-9_x_st 2.09554601
14qII-1_st 2.422851388
14qII-1_x_st 2.007520109
14qII-10_st 1.619070959
14qII-11_st 2.682042227
14qII-12_st 2.191058702
14qII-12_x_st 2.203048518
14qII-13_st 2.222051959

Total number of rows: 25065

Table truncated, full table size 676 Kbytes.




Supplementary file Size Download File type/resource
GSM1486493_15-MCF10A-Exos1.CEL.gz 827.6 Kb (ftp)(http) CEL
Processed data included within Sample table

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