|
| Status |
Public on Jun 05, 2018 |
| Title |
MM at diagnosis, sample 21 |
| Sample type |
RNA |
| |
|
| Source name |
Highly purified PCs from MM patient
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Bone marrow plasma cells
|
| Treatment protocol |
Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL).
|
| Label |
biotin
|
| Label protocol |
Biotinylated single stranded cDNA samples were prepared starting from 100-250 nanograms of total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).
|
| |
|
| Hybridization protocol |
The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 2.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Scanning of the arrays was performed using the GeneChip Scanner 7G.
|
| Description |
hyperdiploid karyotype
|
| Data processing |
Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure. A custom annotation pipeline was applied that combined GENCODE v25 (Ensembl v87) annotations with the CDF (Chip Definition File) version 21 for gene annotations freely available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/genecodeg.asp, in order to withdraw probes that map to regions where ambiguous detection due to transcript overlap might occur. Therefrom, the expression levels of Ensembl genes specific for 10138 unique lncRNAs were obtained.
|
| |
|
| Submission date |
Jan 11, 2018 |
| Last update date |
Jun 26, 2018 |
| Contact name |
Luca Agnelli |
| E-mail(s) |
luca.agnelli@istitutotumori.mi.it, luca.agnelli@gmail.com
|
| Phone |
+390223903581
|
| Organization name |
IRCCS Istituto Nazionale dei Tumori
|
| Department |
Department of Advanced Diagnostics
|
| Street address |
Venezian 1
|
| City |
MILAN |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24507 |
| Series (1) |
| GSE109116 |
A compendium of long non-coding RNAs transcriptional fingerprint in multiple myeloma. |
|
| Relations |
| Alternative to |
GSM3227628 |
