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Sample GSM2255441 Query DataSets for GSM2255441
Status Public on May 12, 2020
Title Adjacent normal tissues from CRC patient 3
Sample type RNA
 
Source name Adjacent normal tissues
Organism Homo sapiens
Characteristics Sex: Male
age: 65y
tissue: normal rectum
tumor location: Rectum
regional lymph nodes metastasis: No
Stage: II
recurrence after operation: No
status after 5 years: Alive
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tissues using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer(Thermo Fisher Scientific, Waltham, MA) and RNA integrity was assessed by standard denaturing agarose gel electrophoresis and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop NanoDrop-1000 Spectrophotometer.
 
Hybridization protocol One μg of each Cy3-labeled, linearly amplified cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
Scan protocol The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
Description histological diagnosis confirmed
Data processing Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs between two samples were identified through Fold Change filtering. Differentially expressed LncRNAs and mRNAs between two groups were identified through Volcano Plot filtering.
 
Submission date Jul 29, 2016
Last update date May 12, 2020
Contact name Xin Zhang
E-mail(s) zhangxin_21@126.com
Organization name Qilu Hospital, Shandong University
Street address 107 Wenhua Xi Road
City Jinan
State/province Shandong
ZIP/Postal code 250012
Country China
 
Platform ID GPL16956
Series (1)
GSE84983 Long noncoding RNA (lncRNA) expression profiles in colorectal cancer tissues and paired adjacent normal tissues

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASHGA5P026943 3.7483876
ASHGA5P032168 7.8744097
ASHGA5P033848 2.5007215
ASHGA5P033259 3.7432163
ASHGA5P031308 2.3258572
ASHGA5P031704 5.5819407
ASHGA5P052532 4.78297
ASHGA5P020436 2.46659
ASHGA5P000568 5.7174873
ASHGA5P046475 6.166943
ASHGA5P022451 7.6218944
ASHGA5P036509 7.8922462
ASHGA5P033872 5.657059
ASHGA5P020989 5.8632517
ASHGA5P023735 7.1837854
ASHGA5P027632 4.92278
ASHGA5P057014 2.5149603
ASHGA5P032500 5.998179
ASHGA5P029189 3.898065
ASHGA5P023560 4.250238

Total number of rows: 4041

Table truncated, full table size 92 Kbytes.




Supplementary file Size Download File type/resource
GSM2255441_A3.txt.gz 2.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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