|
| Status |
Public on Jul 29, 2023 |
| Title |
Sup-B15 cell line |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
SUP-B15 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUP-B15 (CRL-1929)
tissue: Bone marrow
morphology: B lymphoblast
gender: Male
|
| Growth protocol |
Cells grown in RPMI medium supplemented with 10% of fetal bovine serum and with regular passages 2 to 3 times a week
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted with Illustra – Tissue&Cells, GenomicPrep Mini Spin Kit according to manufacturer's instructions
|
| Label |
Cy5-dUTP
|
| Label protocol |
Labeling with either Cy5-dUTP, for SUP-B15 DNA, or Cy3-dUTP, for reference DNA, in Labeling Master Mix composed of 5x reactivation buffer, 10x dNTPs, Exo-Klenow (DNA polymerase), and either Cy5-dUTP or Cy3-dUTP
|
| |
|
| Channel 2 |
| Source name |
Reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
|
| Growth protocol |
Cells grown in RPMI medium supplemented with 10% of fetal bovine serum and with regular passages 2 to 3 times a week
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted with Illustra – Tissue&Cells, GenomicPrep Mini Spin Kit according to manufacturer's instructions
|
| Label |
Cy3-dUTP
|
| Label protocol |
Labeling with either Cy5-dUTP, for SUP-B15 DNA, or Cy3-dUTP, for reference DNA, in Labeling Master Mix composed of 5x reactivation buffer, 10x dNTPs, Exo-Klenow (DNA polymerase), and either Cy5-dUTP or Cy3-dUTP
|
| |
|
| |
| Hybridization protocol |
Incubation in Hybridization Master Mix for 3 minutes, at 95 ºC, followed by 30 minutes at 37 ºC and a 1 minute spin at 6000x g. 100 ul of solution added to hybridization slide and incubated during 24h at 67 ºC and 20 rpm, followed by sequential washes with aCGH/ChIP-on-Chip Wash Buffer 1 and Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 2
|
| Scan protocol |
Slides scanned with DNA Microarray Scanner with SureScan High-Resolution (G2505C, Agilent Technologies, Santa Clara, CA, USA). Images analysed with Agilent Feature Extraction v.12.5.
|
| Description |
SUP-B15 cell line harvested after multiple passages and before cell confluence
|
| Data processing |
Data analysed through CytoGenomics 5.0.2.5 (Agilent Technologies, Santa Clara, CA). Only regions > 1kb were used to build the reference mapping archive using intersetBed and multiIntersectBed functions of R package BEDtools. All statistical analysis made with software GX 14.5 (Agilent Technologies, Santa Clara, CA) and R v.3.6.2.
CNVs calculated using Aberration Detection Method 2 (ADM-2) algorithm with sensibility threshold = 6, aberration filter = 3 and minimum AvgAbsLogRatio = 0.25.
|
| |
|
| Submission date |
Jul 27, 2023 |
| Last update date |
Jul 29, 2023 |
| Contact name |
Caio Bezerra Machado |
| E-mail(s) |
caio.bmachado97@gmail.com
|
| Organization name |
Federal University of Ceará (UFC)
|
| Department |
Drug Research and Development Center (NPDM)
|
| Lab |
Pharmacogenetics Laboratory
|
| Street address |
St. Coronel Nunes de Melo, 1000
|
| City |
Fortaleza |
| State/province |
Ceará |
| ZIP/Postal code |
60430-275 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL16237 |
| Series (1) |
| GSE239416 |
Human SUP-B15 cells: CNV compared to reference genome. |
|
