|
| Status |
Public on Apr 11, 2023 |
| Title |
COACHI_1st_assay |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Epimastigotes (test)
|
| Organism |
Trypanosoma rangeli |
| Characteristics |
strain: Choachi
Stage: Epimastigotes
cell type: Axenic culture
assay: Choachi First Assay
|
| Growth protocol |
Axenic cultures at 28 °C in liver-infusion tryptose medium (LIT) containing 10% fetal calf serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction was performed with the Dneasy Blood & Tissue kit (Qiagen) using 5x107 cells/mL according to the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Fluorescent labeling of gDNA was performed with SureTag DNA Labeling kit (Agilent) following the manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
Epimastigotes (control)
|
| Organism |
Trypanosoma cruzi |
| Characteristics |
strain: CL brener
assay: CLB First Assay
|
| Growth protocol |
Axenic cultures at 28 °C in liver-infusion tryptose medium (LIT) containing 10% fetal calf serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction was performed with the Dneasy Blood & Tissue kit (Qiagen) using 5x107 cells/mL according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Fluorescent labeling of gDNA was performed with SureTag DNA Labeling kit (Agilent) following the manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
After assembling the chamber the Hybridization was performed into the oven rotator rack at 67 ºC, 20 rpm for 24 hours, according to the manufacturer's instructions.
|
| Scan protocol |
The Scanning of the microarray slides was performed in a Agilent G2565CA Microarray Scanning System following the manufacturer's steps described in Oligonucleotide Array-Based CGH for Genomic DNA Analysis - Enzymatic Labeling (Agilent).
|
| Data processing |
Raw data was first normalized using Feature Extraction software (Agilent).
Agilent Genomic Workbench Standard Edition 6.5 was then used to perform CNV interval detection. The QC metrics motif of Workbench 6.5 ensured adequate quality control of the hybridization data. In our study, an array signal which met the requirements if intensity value >50 and signal-to-noise ratio >25 was included in the analysis. The Aberration Detection Method 2 algorithm was used with a threshold of 6 and bin size of 10 to identify genomic variation. Additionally, we applied a relatively stringent post-analysis filter (4 probes, 0.5 log ratio) to ignore small, spurious or low-quality
Logratio.xlsx: represents final processed data, contains the probes, gene name, genomic location, and log2 of (Cy5/Cy3)ratios.
|
| |
|
| Submission date |
Apr 10, 2023 |
| Last update date |
Apr 11, 2023 |
| Contact name |
José Franco Da Silveira |
| E-mail(s) |
jose.franco@unifesp.br
|
| Phone |
+55 (11) 98886-9796
|
| Organization name |
Universidade Federal de São Paulo
|
| Department |
Departamento de Microbiologia, Imunologia e Parasitologia
|
| Lab |
Biologia Molecular de Trypanosoma cruzi
|
| Street address |
Rua Botucatu, 862
|
| City |
São Paulo |
| State/province |
São Paulo |
| ZIP/Postal code |
04023-062 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL32014 |
| Series (1) |
| GSE229354 |
Trypanosoma cruzi CLB vs Trypanosoma rangeli and Trypanosoma conorhini |
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