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Sample GSM2042472 Query DataSets for GSM2042472
Status Public on Nov 08, 2016
Title UCA2
Sample type RNA
 
Source name Colon tissue
Organism Homo sapiens
Characteristics age: 56
gender: Female
location: colon:left
sample type: active ulcerative colitis
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol RNA extraction method
Label Cy3
Label protocol Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled 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.
 
Hybridization protocol 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).
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 v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 19 out of 26 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were identified through Volcano Plot filtering between two groups. Hierarchical Clustering was performed using the R software. GO analysis and Pathway analysis were performed in the standard enrichment computation method
 
Submission date Jan 20, 2016
Last update date Nov 08, 2016
Contact name David Miguel Padua
E-mail(s) davepadua@gmail.com
Organization name UCLA
Department Medicine-Division of Digestive Diseases
Lab .
Street address 10945 Le Conte Ave, PVUB 2114, MC 694907
City Los Angeles
State/province CA
ZIP/Postal code 90027
Country USA
 
Platform ID GPL16956
Series (1)
GSE77013 A long noncoding RNA signature in Ulcerative Colitis

Data table header descriptions
ID_REF
VALUE In GeneSpring GX v12.1, a normalized value is a relative number that comes from the ratio of the comparison between the raw data value of the listed probe and that of the controls.

Data table
ID_REF VALUE
ASHGA5P041796 14.453018
ASHGA5P031496 7.984871
ASHGA5P026943 4.8412523
ASHGA5P018786 10.110445
ASHGA5P000239 6.0085382
ASHGA5P057058 5.1129613
ASHGA5P017384 6.112009
ASHGA5P013553 9.037102
ASHGA5P032168 7.419605
ASHGA5P048339 7.6682262
ASHGA5P033848 6.463428
ASHGA5P040353 8.040908
ASHGA5P039495 13.71777
ASHGA5P025630 6.564476
ASHGA5P019989 6.839298
ASHGA5P053113 12.525873
ASHGA5P022787 4.8736567
ASHGA5P022657 12.953585
ASHGA5P036006 7.3404937
ASHGA5P016582 7.158524

Total number of rows: 13507

Table truncated, full table size 309 Kbytes.




Supplementary file Size Download File type/resource
GSM2042472_UCA2.txt.gz 2.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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