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Sample GSM1553371 Query DataSets for GSM1553371
Status Public on Apr 25, 2016
Title ZC-08
Sample type RNA
Source name primary tumor, lymphnode postive subgroup, replicate 1
Organism Homo sapiens
Characteristics diagnosis: stage IV colorectal cancer
tissue: primary tumor
age: 52y
gender: male
subgroup: lymph node positive
Treatment protocol In our center, 15 patients with resectable mCRC were analyzed, with 7 patients in lymph node negative subgroup and 8 patients in lymph node positive subgroup. Fresh-frozen tissue samples of primary colorectal cancer were obtained. All tissue samples were collected and immediately snap-frozen in liquid nitrogen, and stored at -80˚C until RNA extraction. Written informed consent from each patient was obtained according to the institutional regulations.
Extracted molecule total RNA
Extraction protocol Total RNA isolation was done with TRIzol (Invitrogen, Carlsbad, CA) according to the instructions of the manufacturer. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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 1.65 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 52.8ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2600D) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 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 (G2600D) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression of human primary tumor tissue in lymph node positive subgroup in the resectable stage IV colorectal cancer.
Data processing The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 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 Nov 24, 2014
Last update date Apr 23, 2018
Contact name jianfie fu
Organization name The Second Affiliated Hospital of Zhejiang University School of Medicine
Department Cancer Institute
Lab Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China
Street address 88 Jiefang Road,
City Hangzhou
ZIP/Postal code 310009
Country China
Platform ID GPL17077
Series (1)
GSE63596 The status of lymph node of resectable distant metastaticcolorectal cancer (stage Ⅳ) as a prognostic predictor
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_23_P117082 0.092679024
A_33_P3246448 1.464201
A_21_P0000509 -0.45726013
A_21_P0000744 0.87203884
A_24_P215804 0.64130354
A_23_P110167 -0.7309265
A_33_P3211513 -0.07703209
A_33_P3414202 -0.23102856
A_33_P3316686 -0.17195702
A_33_P3300975 1.2019601
A_33_P3263061 0
A_24_P278460 -0.04502201
A_21_P0014651 0.025001526
A_24_P286898 0.2247405
A_23_P340890 -0.027535439
A_21_P0010885 -0.55488396
A_23_P89762 -0.60160017
A_23_P109034 0.54852486
A_33_P3261031 0.6242032
A_33_P3732466 -0.29544735

Total number of rows: 27597

Table truncated, full table size 639 Kbytes.

Supplementary file Size Download File type/resource
GSM1553371_ZC-08.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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