|
| Status |
Public on Feb 15, 2021 |
| Title |
Non-cancerous Renal Tissue 027 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Non-cancerous renal tissue, donor R027
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: donor R027
gender: Male
age: 55
tissue type: Non-cancerous renal tissue
molecule subtype: Anti-5-mC monoclonal antibody 33D3 immunoprecipitated DNA
|
| Treatment protocol |
Tissue samples were obtained from partial or radical nephrectomy material of patients diagnosed with clear cell renal cell carcinoma. None of the patients had preoperatively received radiotherapy, chemotherapy, or hormone therapy.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Renal tissue samples were homogenized using liquid nitrogen and cryoPREP™ CP02 Impactor with tissue TUBE TT1 (Covaris, Woburg, MA, USA). Homogenized tissue powder were treated for up to 18 h at 55 °C with 10-25 μl of proteinase K and 500 μl of lysis buffer, consisting of 50 mM Tris-HCl pH 8.5, 1 mM EDTA, 0.5% Tween-20. DNA was extracted following the standard phenol-chloroform purification and ethanol precipitation protocol.
|
| Label |
Cy5
|
| Label protocol |
Cyanine-5 and Cyanine-3 labeled DNA was prepared from 26 µl of Anti-5-mC monoclonal antibody 33D3 immunoprecipitated DNA and total DNA respectively using SureTag DNA Labeling Kit acording to manufacturer's protocol (Agilent Technologies) followed by purification using Purification Column provided with the SureTag DNA Labeling Kit. Dye incorporation and DNA yield was measured with NanoDrop 2000.
|
| |
|
| Channel 2 |
| Source name |
Non-cancerous renal tissue, donor R027
|
| Organism |
Homo sapiens |
| Characteristics |
donor id: donor R027
gender: Male
age: 55
tissue type: Non-cancerous renal tissue
|
| Treatment protocol |
Tissue samples were obtained from partial or radical nephrectomy material of patients diagnosed with clear cell renal cell carcinoma. None of the patients had preoperatively received radiotherapy, chemotherapy, or hormone therapy.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Renal tissue samples were homogenized using liquid nitrogen and cryoPREP™ CP02 Impactor with tissue TUBE TT1 (Covaris, Woburg, MA, USA). Homogenized tissue powder were treated for up to 18 h at 55 °C with 10-25 μl of proteinase K and 500 μl of lysis buffer, consisting of 50 mM Tris-HCl pH 8.5, 1 mM EDTA, 0.5% Tween-20. DNA was extracted following the standard phenol-chloroform purification and ethanol precipitation protocol.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-5 and Cyanine-3 labeled DNA was prepared from 26 µl of Anti-5-mC monoclonal antibody 33D3 immunoprecipitated DNA and total DNA respectively using SureTag DNA Labeling Kit acording to manufacturer's protocol (Agilent Technologies) followed by purification using Purification Column provided with the SureTag DNA Labeling Kit. Dye incorporation and DNA yield was measured with NanoDrop 2000.
|
| |
|
| |
| Hybridization protocol |
40 µl of each (Cy5 or Cy3) labeled DNA (80 µl in total) was prepared for hybridization using Oligo aCGH/ChIP-Chip Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized onto Human DNA Methylation 1×244K Microarrays (Agilent Technologies) for 40 hours at 65°C in a rotating hybridization oven (Agilent Technologies).
|
| Scan protocol |
Microarrays were scanned immediately after washing using SureScan microarray scanner (Agilent Technologies).
|
| Description |
DNA methylation profile in non-cancerous renal tissue adjacent primary renal tumor from patient R027
|
| Data processing |
Scanned images were analyzed with Feature Extraction software v10.7.3.1 (Agilent Technologies) using default parameters (protocol ChIP_107_Sep09 (Read Only), grid 023795_D_F_20140814). Background subtracted and spatially detrended signals were obtained.
|
| |
|
| Submission date |
Feb 14, 2021 |
| Last update date |
Feb 15, 2021 |
| Contact name |
Raimonda Kubiliūtė |
| E-mail(s) |
kubiliute.raimonda5@gmail.com
|
| Phone |
864128534
|
| Organization name |
Vilnius University
|
| Department |
Life Sciences Center
|
| Street address |
Sauletekio al., 7
|
| City |
Vilnius |
| State/province |
Saulėtekis |
| ZIP/Postal code |
03106 |
| Country |
Lithuania |
| |
|
| Platform ID |
GPL19930 |
| Series (1) |
| GSE166734 |
DNA methylation profile of cancerous and non-cancerous renal tissues |
|
