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Sample GSM2262721 Query DataSets for GSM2262721
Status Public on Aug 06, 2016
Title MCF10A control
Sample type RNA
Source name MCF10A control
Organism Homo sapiens
Characteristics cell line: Human mammary epithelial cell (MCF10A)
agent: control
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 control
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 8789.529
A_33_P3246448 74.62409
A_33_P3318220 48.972557
A_33_P3236322 33.881596
A_33_P3319925 7.273554
A_21_P0000509 4206.0405
A_21_P0000744 1121.6923
A_24_P215804 128.14278
A_23_P110167 5556.9546
A_33_P3211513 140.41711
A_23_P103349 229.806
A_32_P61480 7.250903
A_33_P3788124 7.24042
A_33_P3414202 220.22182
A_33_P3316686 373.33124
A_33_P3300975 129.6285
A_33_P3263061 8898.807
A_33_P3261373 7.1660824
A_24_P278460 1169.2341
A_21_P0013109 7.1275406

Total number of rows: 50737

Table truncated, full table size 1143 Kbytes.

Supplementary file Size Download File type/resource
GSM2262721_MCF10A_control.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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