NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3259682 Query DataSets for GSM3259682
Status Public on Sep 01, 2018
Title US45103089_253949417580_S02_GE1_1100_56K_1_4
Sample type RNA
 
Source name FFPE
Organism Homo sapiens
Characteristics tissue: Tumor Sample, advanced rectal adenocarcinoma
age at surgery: 81
dworak tumor regression grade: 1
gender: M
Treatment protocol chemoradiation therapy, a combination of capecitabine (825 mg/m2) and radiations (50.4 Gy) provided in 28 fractions in 12 weeks. Clinical staging was accomplished using two physical examinations, endoscopic ultrasound (EUS) and nuclear magnetic resonance (NMR) before the administration of the neoadjuvant treatment. After 8 weeks from the completion of neoadjuvant therapy, surgery was performed
Extracted molecule total RNA
Extraction protocol RNA extraction
Label Cy3
Label protocol Agilent SureTag Labeling kit (Agilent Technologies, Palo Alto, CA, USA), enzymatically label 1.8 µg of amplified cDNA with Cyanine 3-dUTP for 2 hours at 37°C
 
Hybridization protocol Agilent SurePrint G3 Human Gene Expression v2 8x60K Microarray.
Scan protocol Slides were scanned (Agilent SureScan Microarray Scanner) immediately after washing procedure according to the precedure outlined in Agilent one-color Microarray-based gene expression analysis manual.
Description Gene Expression after capecitabine and radiotherapy cycle of 8 weeks
Data processing The scanned images were analyzed with Feature Extraction Software v10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Jul 06, 2018
Last update date Sep 01, 2018
Contact name Lorenzo Ferrando
E-mail(s) lorenzo.ferrando@edu.unige.it
Organization name IRCCS - Ospedale Policlinico San Martino
Department Department of Internal Medicine
Lab Translational Laboratory
Street address Viale Benedetto XV
City Genova
ZIP/Postal code 16132
Country Italy
 
Platform ID GPL17077
Series (1)
GSE116742 Analysis of lncRNAs for the characterization of the response to neoadjuvant chemoradiotherapy

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_23_P117082 12.15090924
A_33_P3246448 6.672549272
A_33_P3318220 7.391200383
A_33_P3236322 10.67296593
A_33_P3319925 8.424810019
A_21_P0000509 10.99160685
A_21_P0000744 8.311233516
A_24_P215804 10.10953029
A_23_P110167 15.05503129
A_33_P3211513 9.663208157
A_23_P103349 10.33583514
A_32_P61480 4.923214184
A_33_P3788124 6.181184377
A_33_P3414202 9.679544557
A_33_P3316686 10.45636636
A_33_P3300975 9.138237588
A_33_P3263061 12.09741327
A_33_P3261373 8.199115952
A_24_P278460 8.579422689
A_21_P0013109 6.746713951

Total number of rows: 50599

Table truncated, full table size 1256 Kbytes.




Supplementary file Size Download File type/resource
GSM3259682_US45103089_253949417580_S02_GE1_1100_56K_1_4.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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