|
| Status |
Public on Jan 02, 2016 |
| Title |
sensitive to AraC_Group 1 [A-03] |
| Sample type |
RNA |
| |
|
| Source name |
Bone Marrow MNC at diagnosis
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 52y
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow mononuclear cells (BM MNCs) from each patient at diagnosis were separated using Ficoll-Paque (GE Healthcare) separation. RNA was isolated from BM MNCsusing Tri Reagent (Sigma), following the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
The samples were labeled using Agilent Quick Amp Labeling Kit one color (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using RNeasy Mini Kit(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.
|
| |
|
| Hybridization protocol |
600ng of labeled cRNA were hybridized on the array using the Hi-RPM large Hybridization Kit (Part No: 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65ยบ C for 16 hours. Hybridized slides were washed using Agilent Gene Expression Wash Buffers Set (Part No: 5188-5327). The hybridized, washed microarray slides were then scanned on a G2505C scanner (Agilent Technologies)
|
| Scan protocol |
Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.7)
|
| Description |
Gene expression at diagnosis
|
| Data processing |
Data extraction from Images was done using Feature Extraction software and Percentile shift Normalization of the data was done in GeneSpring GX.
|
| |
|
| Submission date |
Dec 03, 2013 |
| Last update date |
Jan 02, 2016 |
| Contact name |
Poonkuzhali Balasubramanian |
| E-mail(s) |
[email protected]
|
| Phone |
914162283476
|
| Organization name |
Christian Medical College Vellore
|
| Department |
Department of Haematology
|
| Street address |
Ida Scudder Road
|
| City |
Vellore |
| State/province |
Tamil Nadu |
| ZIP/Postal code |
632004 |
| Country |
India |
| |
|
| Platform ID |
GPL13252 |
| Series (1) |
| GSE52919 |
Gene expression signatures in ex vivo Cytarabine (Ara-C) and Daunorubicin (Dnr) sensitive AML samples |
|
