|
| Status |
Public on Jul 28, 2024 |
| Title |
NSCLC Plasma_Exo-miRNA_50_BASAL |
| Sample type |
RNA |
| |
|
| Source name |
BASAL
|
| Organism |
Homo sapiens |
| Characteristics |
age: 63
histotype: Adc
gender: male
smoke habit: Former smoker
treatment: Nivolumab
# numer of metastatic sites: 2
# brain metastases: no
# liver metastases: no
# prior lines of treatment: 1
performance status: 0
basal or best response: Basal
|
| Treatment protocol |
No treatment
|
| Growth protocol |
No growth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Exosomal total RNA samples were purified from 0.5-1 mL of plasma using the exoRNeasy Serum/Plasma Midi kit (Qiagen, Hilden, Germany) according to manufacturer instructions.
|
| Label |
Cyanine 3-pCp
|
| Label protocol |
Exosomal total RNA samples were processed using the Agilent miRNA complete labeling and hybridization kit (part number 5190-0456) and Agilent miRNA spike-in kit (part number 5190-1934). The Agilent miRNA microarray system was performed using 6 µl or 12 µl of purified total RNA at unknown concentration, based on the plasma input (1 mL or 0.5 mL).
|
| |
|
| Hybridization protocol |
After adding Hyb Spike-In, each sample was hybridized at 55°C for 20 hours on G4872A-070156 Human miRNA Microarray, Release 21.0, 8 x 60K (Agilent Technologies). The supplement of a commercial synthetic DNA poly-A oligonucleotide 3’ labeled pCp-Cy3, was added to the final hybridization mix. The 30-mer synthetic oligonucleotide (HPLC purified) was synthesized by TIB Molbiol s.r.l. (Genova, Italy). The lyophilized oligonucleotide was resuspended at a final concentration of 100 pmol/μL. Before use, an aliquot was taken and through serial dilutions brought to two final concentrations of 50 and 5 amol/μL.
|
| Scan protocol |
Microarrays were scanned (3 microns, 20 bit) on an Agilent microarray scanner (part number G2505C) and data extracted using Agilent feature extraction v.12.0.0.7. QC metrics from feature extraction were used to evaluate the success of the labeling and hybridization.
|
| Data processing |
Pre-processing, filtering and differential expression analysis were carried out using the Limma package, available within Bioconductor. Background correction and between array normalization were carried out using the normexp method, with an offset = 20, and the quantile method, respectively. Replicated probes were then averaged.
|
| |
|
| Submission date |
Aug 08, 2022 |
| Last update date |
Jul 28, 2024 |
| Contact name |
simona coco |
| E-mail(s) |
simona.coco@hsanmartino.it, coco.simona@gmail.com
|
| Phone |
+390105558316
|
| Organization name |
IRCCS Ospedale Policlinico San Martino
|
| Lab |
Lung Cancer Unit
|
| Street address |
L.go R. Benzi, 10
|
| City |
Genova |
| ZIP/Postal code |
16132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21576 |
| Series (1) |
| GSE207715 |
Extracellular vesicles miR-574-5p and miR-181a-5p as prognostic markers in NSCLC patients treated with nivolumab |
|
