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Sample GSM1378998 Query DataSets for GSM1378998
Status Public on May 08, 2014
Title BreastCancer_TripleNegative_C421c
Sample type RNA
Source name Breast tissue
Organism Homo sapiens
Characteristics tissue type: breast cancer
cancer subtype: Triple Negative
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted using Qiagen RNeasy Mini Kit, QIAshredder kit and RNase-Free DNase Set kit (Qiagen, Valencia, CA) following manufacturer's recommendations. The protocol includes homogenization of tissue by grinding in mortor with liquid nitrogen and binding to the RNeasy Mini spin column, then DNase were used to get rid of trace amount of DNA. RNAs were quantified using a NanoDrop-2000 spectrophotometer and their qualities were monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent, Valencia, CA) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen, Valencia, CA) purification. Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (NanoDrop Technologies, Inc).
Hybridization protocol 0.6 ug of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/ug 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 Whole Human Genome Oligo Microarrays (GPL17077) 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 using Agilent stabilization and drying solution.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x60k array slides (Scan Area 61X21 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The data were analyzed by GeneSpring GX (Agilent) using one parameter of subtype, whose values are Luminal A, Luminal B, Triple Negative and normal. Genes were filtered with one-way ANOVA (p<0.05) and fold change >= 2.0.
Submission date May 05, 2014
Last update date Apr 23, 2018
Contact name Xin Qi
Phone 3522945581
Organization name University of Florida
Department Medicinal Chemistry
Lab Health Science Center P5-31
Street address 1600 SW Archer Rd
City Gainesville
State/province FL
ZIP/Postal code 32610
Country USA
Platform ID GPL17077
Series (1)
GSE57297 Identification of significant gene regulations for breast cancer from human tissues
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner -0.23316193
DarkCorner 1.0091047
A_23_P117082 -0.2615738
A_33_P3246448 -1.1735826
A_33_P3318220 1.0338778
A_33_P3236322 0.84119034
A_33_P3319925 -0.03636074
A_21_P0000509 -0.05566311
A_21_P0000744 -0.9498391
A_24_P215804 -1.9532099
A_23_P110167 -0.45844007
A_33_P3211513 0.9083204
A_23_P103349 0.98293114
A_32_P61480 0.75024796
A_33_P3788124 1.2476029
A_33_P3414202 0.950068
A_33_P3316686 0.31005335
A_33_P3300975 -0.7446804
A_33_P3263061 0.68160105
A_33_P3261373 1.9238825

Total number of rows: 50739

Table truncated, full table size 1206 Kbytes.

Supplementary file Size Download File type/resource
GSM1378998_US83800208_253949411413_S02_GE1-v5_10_Apr08_1_4.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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