|
| Status |
Public on Nov 29, 2007 |
| Title |
Peripheralbloodmononuclearcells_ONJ_g |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood mononuclear cells, MM patient with ONJ
|
| Organism |
Homo sapiens |
| Characteristics |
Multiple Myeloma patient with osteonecrosis of the jaw, patient data will be provided in the manuscript
|
| Biomaterial provider |
Noopur Raje, MD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from PBMCs using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA), followed by additional purification using RNeasy from Qiagen.
|
| Label |
biotin
|
| Label protocol |
RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
|
| |
|
| Hybridization protocol |
The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidic station 400 (Affymetrix, Santa Clara, CA, USA) that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe.
|
| Scan protocol |
The DNA chips were then analyzed using a Gene Array Scanner (Affymetrix).
|
| Description |
Multiple Myeloma patient with osteonecrosis of the jaw
|
| Data processing |
CEL files were obtained using Affymetrix Microarray Suite 5.0 software; a DNA Chip Analyzer (DChip) normalized all CEL files to a baseline array with overall median intensity, and the model-based expression (perfect match only) was used to compute expression values.
|
| |
|
| Submission date |
Feb 22, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
sonia vallet |
| E-mail(s) |
sonia_vallet@DFCI.harvard.edu
|
| Phone |
617-632-6554
|
| Fax |
617-632-2140
|
| Organization name |
dana-farber cancer institute
|
| Department |
medical oncology
|
| Street address |
44 binney street
|
| City |
boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE7116 |
Clinical, radiographic, and biomarker characterization of multiple myeloma patients with osteonecrosis of the jaw. |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
