NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2070259 Query DataSets for GSM2070259
Status Public on Oct 30, 2017
Title Wnt- rectal tumor 5 [GE]
Sample type RNA
 
Channel 1
Source name Surgically removed rectum
Organism Homo sapiens
Characteristics Sex: Female
age: 55
tissue: Rectal adenocarcinoma
Stage: NA
grade: 1
Growth protocol Not applicable
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy5
Label protocol 2μg each of total RNA from tumors along with equal quantity of universal reference RNA (pooled up RNA from 11 cell lines (Bashyam et al., 2005)) were differentially labeled with Cy5 and Cy3 dyes using Quickamp labeling kit (Agilent Technologies, CA, USA) following manufacturer's instructions
 
Channel 2
Source name pooled 11 cell line
Organism Homo sapiens
Characteristics reference: Universal reference RNA
Growth protocol Not applicable
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy3
Label protocol 2μg each of total RNA from tumors along with equal quantity of universal reference RNA (pooled up RNA from 11 cell lines (Bashyam et al., 2005)) were differentially labeled with Cy5 and Cy3 dyes using Quickamp labeling kit (Agilent Technologies, CA, USA) following manufacturer's instructions
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
Scan protocol Scanned on an Agilent G2505B scanner
Images were quantified using Agilent Feature Extraction Software (version v10.7)
Description 1055
Microsatellite stable Wnt- rectal adenocarcinoma
Data processing Agilent Feature Extraction Software (v10.7) was used for background subtraction and LOWESS normalization
 
Submission date Feb 24, 2016
Last update date Oct 30, 2017
Contact name Murali Dharan Bashyam
E-mail(s) bashyam@cdfd.org.in
Organization name CDFD
Street address MJ MARKET
City HYDERABAD
State/province (Click to Select US State)
ZIP/Postal code 500001
Country India
 
Platform ID GPL4133
Series (2)
GSE78250 Early-onset sporadic rectal cancer : Wnt- vs. Wnt+ rectal tumor [GE]
GSE79330 Early-onset sporadic rectal cancer : Wnt- vs. Wnt+ rectal tumor

Data table header descriptions
ID_REF
VALUE normalized log10 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
12 -3.30E-01
13 2.45E-02
14 7.00E-02
15 -1.63E-01
16 -7.17E-02
17 9.37E-01
18 -3.51E-01
19 1.34E-01
20 1.23E-01
21 0.00E+00
22 -2.71E-03
23 0.00E+00
24 -1.12E-01
25 -2.55E-01
26 5.12E-01
27 1.61E-01
28 0.00E+00
29 0.00E+00
30 6.57E-01
31 7.22E-02

Total number of rows: 43376

Table truncated, full table size 640 Kbytes.




Supplementary file Size Download File type/resource
GSM2070259_47_GE.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap