|
| Status |
Public on Mar 11, 2021 |
| Title |
Tumor vs Normal patient ID 149 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: GI Tract / Rectum
gender: Female
age: 54
|
| 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 GI - 149
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 |
|
