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Sample GSM1569049 Query DataSets for GSM1569049
Status Public on Apr 28, 2015
Sample type RNA
Source name primary culture cells of human mammary epithelium HMEC expressing GLI1.
Organism Homo sapiens
Characteristics cell type: primary human mammary epithelium cells (HMEC)
genotype/variation: expressing GLI1
Extracted molecule total RNA
Extraction protocol Not provided.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Quick Amplification 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 (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray (G4851B) 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 (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Dec 19, 2014
Last update date Apr 29, 2015
Contact name Kenji Kasai
Organization name Aichi Medical University School of Medicine
Department Department of Pathology
Street address 1-1 Yazakokarimata
City Nagakute
State/province Aichi
ZIP/Postal code 480-1195
Country Japan
Platform ID GPL17077
Series (1)
GSE64350 GLI1-regulated genes in human mammary epithelial cells and human breast cancer cells

Data table header descriptions
VALUE Normalized signal intensity

Data table
(+)E1A_r60_1 839.035
(+)E1A_r60_3 0.014
(+)E1A_r60_a104 0.016
(+)E1A_r60_a107 0.095
(+)E1A_r60_a135 0.773
(+)E1A_r60_a20 1.691
(+)E1A_r60_a22 5.100
(+)E1A_r60_a97 28.580
(+)E1A_r60_n11 112.283
(+)E1A_r60_n9 211.193
3xSLv1 0.009
A_19_P00315452 3.781
A_19_P00315459 0.198
A_19_P00315482 0.030
A_19_P00315492 0.054
A_19_P00315493 0.013
A_19_P00315502 20.641
A_19_P00315506 23.503
A_19_P00315518 0.064
A_19_P00315519 0.009

Total number of rows: 50739

Table truncated, full table size 972 Kbytes.

Supplementary file Size Download File type/resource
GSM1569049_US09503747_253949430567_S01_GE1_107_Sep09_1_2.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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