|
| Status |
Public on Jun 18, 2019 |
| Title |
MM.268: MM at diagnosis, sample 30 |
| Sample type |
RNA |
| |
|
| Source name |
Highly purified PCs from MM patient
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone marrow plasma cells
diagnosis: Multiple myeloma (MM)
genotype/variation: non-hyperdiploid karyotype, no major IgH (14q32) chromosomal translocations
|
| 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.
|
| 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 Human GeneChip Gene 2.0 ST transcript annotations freely available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/ genecodet.asp, in order to withdraw probes that map to regions where ambiguous detection due to transcript overlap might occur. Only genes identified by probesets with 4 or more specifc probes within were retained. The gained CDF results a umich GENCODEG-like annotation that retains only unambiguous signals for lncRNA and coding genes that partially overlap in thier genomic position.
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| |
|
| Submission date |
Jun 26, 2018 |
| Last update date |
Jun 18, 2019 |
| 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 |
GPL25249 |
| Series (1) |
| GSE116294 |
Deregulated high expression of NEAT1 lncRNA in multiple myeloma is unrelated to molecular features and clinical outcome |
|
| Relations |
| Alternative to |
GSM2932353 |
