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Sample GSM1103695 Query DataSets for GSM1103695
Status Public on Jan 01, 2017
Title Responder - sample 68
Sample type RNA
 
Source name Pre Treatment biopsies
Organism Homo sapiens
Characteristics tissue: CRC sample
disease state: Rectal cancer
name: E139
age: 66
Sex: Female
class: Responder
Treatment protocol Pre CRT research biopsies (2-3 mm3) were collected during the initial diagnostic endoscopy, immediately frozen and stored in a liquid nitrogen tank.
Growth protocol No growth protocols were used
Extracted molecule total RNA
Extraction protocol RNA was extracted by phenol/chloroform extraction (TRIzol; Invitrogen) prior to further purification by column chromatography (RNeasy Mini kit; Qiagen). RNA integrity was then assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies)
Label biotin
Label protocol Agilent Whole Human Genome GE44K microarray platform was used. Standard Agilent RNA extraction and hybridization protocols were used.
 
Hybridization protocol Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
Scan protocol Arrays were scanned using the Agilent Scanner G2505B
Description Gene expression data from CRC patients at diagnosis
Data processing The data were normalized using R software [www.r-project.org] with BioConductor package [www.bioconductor.org] "Agi4x44PreProcess" (intra-array[Multiplicatively Detrended] and inter-array [Quantile] normalization).
 
Submission date Mar 21, 2013
Last update date Jan 01, 2017
Contact name Andrea Zangrando
E-mail(s) andrea.zangrando@unipd.it
Organization name University of Padova
Department Woman and Child's Health
Lab Hemato-Oncology
Street address Via Giustiniani, 3
City Padova
ZIP/Postal code 35138
Country Italy
 
Platform ID GPL4133
Series (1)
GSE45404 Integrative computational biology and molecular determinants of rectal cancer resistance to chemoradiotherapies

Data table header descriptions
ID_REF
VALUE normalized signal intensity

Data table
ID_REF VALUE
1 95471.05263
2 26.80894737
3 27.34644737
4 27.74447368
5 28.01894737
6 28.30868421
7 28.59973684
8 28.71078947
9 28.83
10 28.83
11 28.83
12 621.3421053
13 34.27842105
14 1535.328947
15 28.30868421
16 10307.36842
17 381.2868421
18 116.4552632
19 110368.4211
20 26.80894737

Total number of rows: 45015

Table truncated, full table size 766 Kbytes.




Supplementary file Size Download File type/resource
GSM1103695_UniversityPadova_251485050814_E139_GE1_105_Dec08_1_1.txt.gz 7.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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