|
| Status |
Public on Jun 05, 2024 |
| Title |
HCT-116 colorectal adenocarcinoma cell line, single array |
| Sample type |
genomic |
| |
|
| Source name |
confluent cell cultures
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colorectal adenocarcinoma cell line
Sex: male
age: --
|
| Treatment protocol |
None
|
| Growth protocol |
CACO-2 and HT-29 cell lines were maintained in Dulbecco’s Modified Eagle Medium (DMEM 1X; GIBCO, Cat. No. 31965-023 containing 4.5 g/L of D-glucose) supplemented with 10-20% fetal bovine serum (Cat. No. 10270-106; Life Technologies) and 1% penicillin-streptomycin (100 unit/ml penicillin and 100 μg/ml streptomycin) (Cat. No. 15140-122; Life Technologies). HCT-116 cell line was maintained in McCoy's 5a Medium Modified supplemented with 10% fetal bovine serum and 1% of penicillin-streptomycin. The cell cultures were grown in flasks (25 cm2) and incubated at 37 °C in humidified atmosphere with 5% of CO2 and 95% of air.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was extracted from Caco-2, HCT-116 and HT-29 colorectal adenocarcinoma cell linse using the QIAamp DNA Mini Kit (COD.51304 QIAGEN Milan, Italy) according to the manufacturer’s instructions. The concentration and the quality of the DNA were determined using NanoDrop spectrophotometer.
|
| Label |
biotin
|
| Label protocol |
Amplification and labeling were performed according to the protocol supplied by the Affymetrix for SNP 6.0 arrays. 500 ng of gDNA was digested with NspI and StyI restriction enzymes, ligated to respectively NspI and StyI adaptors, amplified by PCR using a single primer. PCR products were purified and the amplicons were quantified using a NanoDrop spectrophotometer. 40-70 µg of purified amplicons were fragmented and biotin end-labeled.
|
| |
|
| Hybridization protocol |
Biotin-labeled fragments were hybridized to a Genechip Affymetrix SNP 6.0 arrays at 50°C for 16-18 hours in a GeneChip® Hybridization Oven 640 (Affymetrix, Inc.). Washing and staining with streptavidin-phycoerthrin was performed in a GeneChip® Fluidics Station 450 (Affymetrix, Inc.).
|
| Scan protocol |
Arrays were scanned with a GeneChip® Scanner 3000 7G (Affymetrix, Inc.) and raw data processing was performed using the “GeneChip Operating Software”.
|
| Data processing |
Data processing was performed by the software "Genotyping Console v3.0.1 ". The following algorithms were used: 1) SNP 6.0 Birdseed v2 algorithm for genotyping, 2) BRLMM-P-Plus algorithm and Hidden Markov Model with regional GC correction for copy number analysis, 3) the LOH algorithm.
Intensity Data files (.cel) and Copy Number Data files (.cnchp) are provided.
|
| |
|
| Submission date |
May 08, 2024 |
| Last update date |
Jun 05, 2024 |
| Contact name |
Daniele F Condorelli |
| E-mail(s) |
daniele.condorelli@unict.it, vincenza.barresi@unict.it
|
| Organization name |
University of Catania
|
| Department |
Biomedical and Biotechnological Sciences
|
| Lab |
Medical Biochemistry
|
| Street address |
Via S. Sofia 64
|
| City |
Catania |
| State/province |
Italy |
| ZIP/Postal code |
95125 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE267025 |
SNP arrays in colorectal adenocarcinoma cell lines |
|
