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Sample GSM1424543 Query DataSets for GSM1424543
Status Public on Nov 01, 2014
Title KP-MRT-RY_negative
Sample type RNA
Source name Cell line
Organism Homo sapiens
Characteristics cell line: KP-MRT-RY
cell type: CD146-
mcam: negative
Treatment protocol Purified cells were sorted by FACSAriaⅡusing anti-human CD146 antibody (Miltenyi)
Growth protocol All cell lines were cultured in RPMI-1640 medium containing penicillin, streptomycin, L-glutamine, and 10% heat-inactivated fetal bovine serum (FBS) at 37 °C, and 5% CO2 humidified incubator.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the RNeasy mini kit (Qiagen) following the manufacturer's recommendations.
Label Cy3
Label protocol cDNA was generated from 2.0 ng RNA using Ribo-SPIA technology (NuGEN Technologies). Cyanine-3 (Cy3) labeled cDNA was generated using the Genomic DNA Enzymatic Labeling Kit (Agilent) according to the manufacturer's instructions. Quality of labeled cDNA was checked by 2100 Bioanalyzer. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 3.0 ug of Cy3-labelled cDNA (specific activity >25.0 pmol Cy3/ug cDNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer 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 8×60K Microarray 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 (Scan Area 71x21.6 mm, Scan resolution 10um).
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Jul 02, 2014
Last update date Apr 23, 2018
Contact name Seishiro Nodomi
Phone +81-75-751-3291
Organization name Graduate School of Medicine, Kyoto University
Department Pediatrics
Street address 54 Kawahara-cho, Shogoin, Sakyo-ku
City Kyoto
ZIP/Postal code 606-8507
Country Japan
Platform ID GPL17077
Series (1)
GSE59025 The difference of gene expression signatures between CD146+ and CD146- cells in malignant rhabdoid tumor
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 0.07
DarkCorner -3.09
A_23_P117082 0.01
A_33_P3246448 4.61
A_33_P3318220 -0.52
A_33_P3236322 0.20
A_33_P3319925 0.06
A_21_P0000509 2.54
A_21_P0000744 0.81
A_24_P215804 0.17
A_23_P110167 0.05
A_33_P3211513 0.45
A_23_P103349 -0.25
A_32_P61480 -0.16
A_33_P3788124 -0.07
A_33_P3414202 1.07
A_33_P3316686 1.52
A_33_P3300975 -0.78
A_33_P3263061 -0.41
A_33_P3261373 -0.03

Total number of rows: 50739

Table truncated, full table size 941 Kbytes.

Supplementary file Size Download File type/resource
GSM1424543_6-RY-.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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