GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3259705 Query DataSets for GSM3259705
Status Public on Sep 01, 2018
Title US45103089_253949440416_S01_GE1_1100_88K_2_1
Sample type RNA
Source name FFPE
Organism Homo sapiens
Characteristics tissue: Tumor Sample, advanced rectal adenocarcinoma
age at surgery: 50
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
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
VALUE Normalized signal intensity

Data table
A_23_P117082 10.07063965
A_33_P3246448 8.228273427
A_33_P3318220 9.36165865
A_33_P3236322 14.2169873
A_33_P3319925 10.21369556
A_21_P0000509 15.64394833
A_21_P0000744 8.265317978
A_24_P215804 6.053601485
A_23_P110167 12.54316711
A_33_P3211513 9.123483344
A_23_P103349 8.956254692
A_32_P61480 4.677160685
A_33_P3788124 6.889001733
A_33_P3414202 12.39764655
A_33_P3316686 10.07452502
A_33_P3300975 10.01931732
A_33_P3263061 9.83983885
A_33_P3261373 10.39183784
A_24_P278460 6.74413679
A_21_P0013109 8.268908289

Total number of rows: 50599

Table truncated, full table size 1256 Kbytes.

Supplementary file Size Download File type/resource
GSM3259705_US45103089_253949440416_S01_GE1_1100_88K_2_1.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