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Sample GSM1941517 Query DataSets for GSM1941517
Status Public on May 18, 2016
Title rectal cancer_with liver metastasis_original [Exp 3]
Sample type RNA
 
Source name rectal cancer_with liver metastasis
Organism Homo sapiens
Characteristics subject status: colorectal cancer (CRC) patient with liver metastasis
age (yrs): 62
gender: M
tissue: peripheral blood
Treatment protocol Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated for 6 or 24 hours at 37C in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. 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 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 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 Whole Human Genome Oligo Microarrays (G4112A) 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 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description lncRNAs and mRNAs expression in the rectal cancer tissue of CRC patients with liver metastasis
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) 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 16, 2015
Last update date May 18, 2016
Contact name Dong Chen
E-mail(s) chendongking@163.com
Organization name First Affiliated Hospital, Zhejiang University
Street address 79# Qingchun Rd
City Hangzhou
ZIP/Postal code 310003
Country China
 
Platform ID GPL16956
Series (1)
GSE75050 Genome-wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASHGA5P058197 2.3249023
ASHGA5P007773 10.577228
ASHGA5P031162 5.1177635
ASHGA5P041796 14.003344
ASHGA5P006930 7.9468727
ASHGA5P031496 7.8422365
ASHGA5P050699 12.181876
ASHGA5P035298 4.908987
ASHGA5P014867 2.3249023
ASHGA5P008172 7.3515015
ASHGA5P047663 5.6964006
ASHGA5P012016 8.254259
ASHGA5P007747 9.233944
ASHGA5P026943 6.6834207
ASHGA5P035562 4.133211
ASHGA5P018786 12.016506
ASHGA5P001180 9.473915
ASHGA5P023786 2.3249023
ASHGA5P021269 6.3317637
ASHGA5P000239 3.7301247

Total number of rows: 58944

Table truncated, full table size 1353 Kbytes.




Supplementary file Size Download File type/resource
GSM1941517_EXP3.txt.gz 2.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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