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Sample GSM5151386 Query DataSets for GSM5151386
Status Public on Mar 11, 2021
Title Tumor vs Normal patient ID 183
Sample type RNA
 
Channel 1
Source name Cancer tissue
Organism Homo sapiens
Characteristics tissue: Colon
gender: Male
age: 66
Extracted molecule total RNA
Extraction protocol The tissue biopsies were lysed with a Polytron, by homogenization in the lysis buffer RLT Plus provided in the kit, and DNA was obtained with a specific affinity silica matrix column, specifically retaining the DNA, whereas RNAs and proteins were collected from the through flow. DNA was washed and eluted. The through flow containing RNAs was mixed with tri-reagent and, subsequently, RNA was obtained by isopropanol precipitation. This procedure enables the collection of all types of RNAs, including mRNAs and small microRNA species. RNAs pelleted through centrifugation were washed with ethanol 75% and solved in nuclease-free water
Label Cy5/Cy3
Label protocol Of each tumor and normal tissue, 100 ng total RNA was used to generate double-stranded complementary DNA using MMLV reverse transcriptase and oligo DT primers coupled with the promoter sequence of T7 RNA. Probe labeling and linear amplification were generated using Agilent Technologies reagents and T7 RNA polymerase that generated labeled complementary labeled RNAs (tumor labeled with Cy5 and normal tissue with complementary RNAs with Cy3).
 
Channel 2
Source name Organ-matched normal tissue
Organism Homo sapiens
Characteristics tissue: Rectal/colon mucosa
Extracted molecule total RNA
Extraction protocol The tissue biopsies were lysed with a Polytron, by homogenization in the lysis buffer RLT Plus provided in the kit, and DNA was obtained with a specific affinity silica matrix column, specifically retaining the DNA, whereas RNAs and proteins were collected from the through flow. DNA was washed and eluted. The through flow containing RNAs was mixed with tri-reagent and, subsequently, RNA was obtained by isopropanol precipitation. This procedure enables the collection of all types of RNAs, including mRNAs and small microRNA species. RNAs pelleted through centrifugation were washed with ethanol 75% and solved in nuclease-free water
Label Cy3/Cy5
Label protocol Of each tumor and normal tissue, 100 ng total RNA was used to generate double-stranded complementary DNA using MMLV reverse transcriptase and oligo DT primers coupled with the promoter sequence of T7 RNA. Probe labeling and linear amplification were generated using Agilent Technologies reagents and T7 RNA polymerase that generated labeled complementary labeled RNAs (tumor labeled with Cy5 and normal tissue with complementary RNAs with Cy3).
 
 
Hybridization protocol Hybridizations were performed as dual-dye-swapped (direct and inversed labeling) experiments with direct cohybridization of equal amounts of labeled tumor and normal probes.
Scan protocol Microarrays were read using the Agilent 2000 scanner version C.
Description Tumor vs Normal Colon - 183
All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.
Data processing Data was processed with Agilent Feature extractions software
 
Submission date Mar 10, 2021
Last update date Mar 11, 2021
Contact name Shai Magidi
E-mail(s) shai.magidi@winconsortium.org
Organization name WIN Consortium
Street address rue Guy Moquet
City Villejuif
ZIP/Postal code 94800
Country France
 
Platform ID GPL14550
Series (1)
GSE168621 Dual tumor and normal biopsies from various cancer patients

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio representing tumor/normal

Data table
ID_REF VALUE
A_24_P365721 -0.462335532
A_33_P3327587 -0.073279286
A_23_P16110 0.010094156
A_33_P3336696 -1.308756444
A_23_P5415 -0.95988262
A_19_P00322834 0.61627187
A_24_P141707 0.071586125
A_33_P3262452 -1.307806399
A_23_P397417 -0.960056709
A_33_P3390743 0.360510886
A_19_P00802265 -0.440184352
A_33_P3241696 0.102190926
A_23_P329835 -0.482548686
A_33_P3409620 0.011329008
A_23_P79134 0.566556915
A_23_P427148 0.543713806
A_23_P82334 -1.164650139
A_23_P212968 -3.098733549
A_24_P366787 1.25135541
A_19_P00811284 -0.976058848

Total number of rows: 42405

Table truncated, full table size 1040 Kbytes.




Supplementary file Size Download File type/resource
GSM5151386_183.tsv.gz 1.8 Mb (ftp)(http) TSV
GSM5151386_AFE_183_normal-Cy5_vs_tumor-Cy3_Rev.txt.gz 6.0 Mb (ftp)(http) TXT
GSM5151386_AFE_183_tumor-Cy5_vs_normal-Cy3.txt.gz 6.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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