|
| Status |
Public on Aug 25, 2023 |
| Title |
HCC1395-rep1 |
| Sample type |
genomic |
| |
|
| Source name |
Breast carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC1395
gender: Female
tissue: Breast tumor
disease state: carcinoma
|
| Growth protocol |
HCC1395 cells were cultured in RPMI-1640 + 10% FBS. HCC1395BL cells were cultured in IMDM + 20% FBS. All cells were maintained at 37°C with 5% CO2 and subcultured every 2–3 days according to ATCC-recommended procedures.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Pellets of cultured cells were lysed in a solution of 2% TritonX-100/0.1% SDS/0.1 M NaCl/10 mM Tris/1 mM EDTA and genomic DNA extracted over repeated rounds of treatment with a mixture of glass beads and phenol-chloroform-isoamyl alcohol. The final aqueous layer was further treated with chloroform-indoleacetic acid followed by RNAse treatment and DNA precipitation using sodium acetate (3 M, pH 5.2) and ice-cold ethanol.
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
200ng of genomic DNA was whole-genome amplified in a 24-hour reaction at 37°C using Multi-Sample Amplification Mixes 1 and 2 (MA1 and MA2) and Multi- Sample Master Mix (MSM). After incubation, the amplified DNA was fragmented with Fragmentation Solution (FMS), precipitated with isopropanol and Preciptitation Solution (PM1), and resuspended in Resuspension Solution (RA1).
|
| |
|
| Hybridization protocol |
DNA resuspended in RA1 was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Te-Flow chamber rack system (Tecan, Maennedorf, Switzerland).
|
| Scan protocol |
After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour, and scanned using the iScan System (Illumina).
|
| Description |
Genomic DNA extracted from cell lines was genotyped using Infinium CytoSNP-850K Genotyping BeadChips (Illumina).
CRL-2324 cell line
|
| Data processing |
Genomic DNA extracted from cell lines was genotyped using Infinium CytoSNP-850K Genotyping BeadChips (Illumina).
|
| |
|
| Submission date |
Aug 25, 2022 |
| Last update date |
Aug 25, 2023 |
| Contact name |
Wenming Xiao |
| Organization name |
Center for Drug Evaluation and Research, FDA
|
| Department |
Office of New Drugs
|
| Street address |
10903 New Hampshire Avenue
|
| City |
Silver Spring |
| State/province |
MD |
| ZIP/Postal code |
20993 |
| Country |
USA |
| |
|
| Platform ID |
GPL31039 |
| Series (1) |
| GSE212051 |
Evaluation of somatic copy number variation detection by NGS techonologies and bioinformatics tools |
|
