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Sample GSM1486492 Query DataSets for GSM1486492
Status Public on Aug 27, 2014
Title MDA-MB-231 exos_2
Sample type RNA
 
Source name breast carcinoma cells
Organism Homo sapiens
Characteristics cell/tissue type: cancer exosomes
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 2.648055722
14qI-1_st 4.696241308
14qI-1_x_st 2.952726574
14qI-2_st 2.187574879
14qI-3_x_st 1.452538579
14qI-4_st 1.844256038
14qI-4_x_st 2.192953197
14qI-5_st 2.349039259
14qI-6_st 1.781293182
14qI-7_st 2.280642458
14qI-8_st 3.08768357
14qI-8_x_st 2.555497627
14qI-9_x_st 1.896470686
14qII-1_st 1.980517418
14qII-1_x_st 1.909743521
14qII-10_st 1.730658218
14qII-11_st 1.692551809
14qII-12_st 1.980517418
14qII-12_x_st 2.104044334
14qII-13_st 3.59285594

Total number of rows: 25065

Table truncated, full table size 676 Kbytes.




Supplementary file Size Download File type/resource
GSM1486492_14-MDA-MB-231-Exos-2.CEL.gz 865.7 Kb (ftp)(http) CEL
Processed data included within Sample table

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