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Sample GSM3259680 Query DataSets for GSM3259680
Status Public on Sep 01, 2018
Title US45103089_253949417580_S01_GE1_1100_21K_2_3
Sample type RNA
Source name FFPE
Organism Homo sapiens
Characteristics tissue: Tumor Sample, advanced rectal adenocarcinoma
age at surgery: 39
dworak tumor regression grade: 3
gender: F
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 12.5471417
A_33_P3246448 8.013201523
A_33_P3318220 9.107073114
A_33_P3236322 11.50763112
A_33_P3319925 7.742836922
A_21_P0000509 13.06492432
A_21_P0000744 9.564536896
A_24_P215804 9.879409621
A_23_P110167 14.71470406
A_33_P3211513 11.30906132
A_23_P103349 9.613288761
A_32_P61480 4.814622904
A_33_P3788124 7.703926434
A_33_P3414202 11.75183133
A_33_P3316686 10.83799839
A_33_P3300975 10.02726554
A_33_P3263061 10.9006555
A_33_P3261373 8.462277192
A_24_P278460 9.187916924
A_21_P0013109 5.922389214

Total number of rows: 50599

Table truncated, full table size 1256 Kbytes.

Supplementary file Size Download File type/resource
GSM3259680_US45103089_253949417580_S01_GE1_1100_21K_2_3.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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