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Sample GSM2262722 Query DataSets for GSM2262722
Status Public on Aug 06, 2016
Title MCF10A blackcurrant
Sample type RNA
Source name MCF10A blackcurrant
Organism Homo sapiens
Characteristics cell line: Human mammary epithelial cell (MCF10A)
agent: black currant extract
Treatment protocol MCF10A cells were purchased from American Type Culture Collection. The MCF10A were routinely cultured in mammary epithelial cell growth medium kit at 37ºC in 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by using the RNeasy mini kit (Qiagen, Tokyo, Japan).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).
Description Gene expression treatment with cassis extract
Data processing The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Aug 05, 2016
Last update date Aug 06, 2016
Contact name Naoki Nanashima
Organization name Aomori University of Health and Welfare
Department Department of Nutrition
Street address 58-1 Mase, Hamadate
City Aomori
State/province Aomori
ZIP/Postal code 030-8505
Country Japan
Platform ID GPL17077
Series (1)
GSE85235 Effects of black currant extract on gene expression on MCF10A

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_23_P117082 6394.599
A_33_P3246448 18.80944
A_33_P3318220 17.044043
A_33_P3236322 8.887539
A_33_P3319925 8.888749
A_21_P0000509 3192.0686
A_21_P0000744 631.26215
A_24_P215804 48.9097
A_23_P110167 4167.356
A_33_P3211513 111.71418
A_23_P103349 9.64942
A_32_P61480 8.83325
A_33_P3788124 8.818329
A_33_P3414202 170.64908
A_33_P3316686 352.1974
A_33_P3300975 125.895744
A_33_P3263061 8295.187
A_33_P3261373 8.722318
A_24_P278460 639.2655
A_21_P0013109 8.674995

Total number of rows: 50737

Table truncated, full table size 1138 Kbytes.

Supplementary file Size Download File type/resource
GSM2262722_MCF10A_blackcurrant.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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