|
| Status |
Public on Dec 06, 2023 |
| Title |
Patient 28_lt34 |
| Sample type |
RNA |
| |
|
| Source name |
Anaplastic Large Cell Lymphoma
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: F
age: 31
alk phenotype: neg
|
| Treatment protocol |
Specimens from ALCL affected patients were included in this study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Formalin-fixed, paraffin-embedded (FFPE) tissues of ALCL were reviewed by different pathologists. For RNA purification, five 5um FFPE slides were cut for each tumor. Total RNA was extracted by Maxwell® RSC RNA FFPE kit (Promega). RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of 39 genes by a NanoString Custom Panel called VF_150921 (NanoString Technologies).
|
| Label |
Molecular barcode on reporter probe
|
| Label protocol |
RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.
|
| |
|
| Hybridization protocol |
RNA was hybridized to capture and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a flourescent barcode specific for each transcript.
|
| Scan protocol |
Scanning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.
|
| Description |
Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol
|
| Data processing |
Data were collected as NanoString RCC files. The data were normalized using 3 HK genes (COG7, DNAJC14, ERCC3). Raw values correspond to the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted only from coding genes counts to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, three reference genes were selected among the 15 available in the panel based on the lowest coefficients of variation (CV= ratio between standard deviations and mean counts across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls.
|
| |
|
| Submission date |
Nov 07, 2022 |
| Last update date |
Dec 06, 2023 |
| Contact name |
Benedetta Donati |
| E-mail(s) |
benedetta.donati@ausl.re.it
|
| Organization name |
Azienda USL- IRCCS di Reggio Emilia
|
| Lab |
Laboratory of Translational Research
|
| Street address |
Viale Risorgimento, 80
|
| City |
Reggio Emilia |
| ZIP/Postal code |
42123 |
| Country |
Italy |
| |
|
| Platform ID |
GPL32835 |
| Series (1) |
| GSE217426 |
Expression signature characteristic of Anaplastic Large Cell Lymphoma (ALCL) patients |
|
