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Sample GSM1486488 Query DataSets for GSM1486488
Status Public on Aug 27, 2014
Title 4T1 exos_2
Sample type RNA
 
Source name breast carcinoma cells
Organism Mus musculus
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 1.779926388
14qI-1_st 2.254392336
14qI-1_x_st 1.818502492
14qI-2_st 1.618745167
14qI-3_x_st 1.569274271
14qI-4_st 1.18267935
14qI-4_x_st 2.36433809
14qI-5_st 1.457136949
14qI-6_st 1.396667795
14qI-7_st 1.857637021
14qI-8_st 1.768495575
14qI-8_x_st 1.61139124
14qI-9_x_st 1.609832131
14qII-1_st 1.950630929
14qII-1_x_st 2.148862262
14qII-10_st 1.754211776
14qII-11_st 1.745085441
14qII-12_st 1.950630929
14qII-12_x_st 1.576431631
14qII-13_st 2.034359735

Total number of rows: 25065

Table truncated, full table size 676 Kbytes.




Supplementary file Size Download File type/resource
GSM1486488_08-4T1-Exos-2.CEL.gz 800.5 Kb (ftp)(http) CEL
Processed data included within Sample table

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