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Sample GSM5151388 Query DataSets for GSM5151388
Status Public on Mar 11, 2021
Title Tumor vs Normal patient ID 223
Sample type RNA
 
Channel 1
Source name Cancer tissue
Organism Homo sapiens
Characteristics tissue: Head and Neck
gender: Female
age: 65
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: Tongue
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 Head and Neck - 223
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 1.404307301
A_33_P3327587 0.971351319
A_23_P16110 -1.017824298
A_33_P3336696 1.541187156
A_23_P5415 -0.102396713
A_19_P00322834 0.132439224
A_24_P141707 -1.610128482
A_33_P3262452 0.295417247
A_23_P397417 -0.187548856
A_33_P3390743 -0.006777895
A_19_P00802265 0.258483009
A_33_P3241696 -0.44574164
A_23_P329835 -1.895408008
A_33_P3409620 -0.439016745
A_23_P79134 0.677794585
A_23_P427148 0.389475327
A_23_P82334 -0.205602316
A_23_P212968 3.591353641
A_24_P366787 -0.451772301
A_19_P00811284 -0.221045688

Total number of rows: 42405

Table truncated, full table size 1054 Kbytes.




Supplementary file Size Download File type/resource
GSM5151388_223.tsv.gz 1.8 Mb (ftp)(http) TSV
GSM5151388_AFE_223_normal-Cy5_vs_tumor-Cy3_Rev.txt.gz 6.0 Mb (ftp)(http) TXT
GSM5151388_AFE_223_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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