|
| Status |
Public on Feb 08, 2012 |
| Title |
SET2_ctr_3h_2 |
| Sample type |
RNA |
| |
|
| Source name |
SET2 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment group: ctr_3h
genotype: MUTATED FOR JAK2V617F
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA, including small RNAs, was extracted using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
|
| Label |
biotin
|
| Label protocol |
Total RNA (500ng for samples) was labeled using the FlashTag Biotin HSR kit (Genisphere)
|
| |
|
| Hybridization protocol |
Total labeled RNA was hybridized to the Affymetrix Genechip miRNA array 1.0 using manufacturer's protocols.
|
| Scan protocol |
Image files from scanning (.dat and .cel files) were generated with Affymetrix Expression Console package.
|
| Description |
SET2 control cells collected at 3h (replicate #2)
|
| Data processing |
Signal reconstruction was performed using the RMA algorithm as implemented in Bioconductor affy package. All chip probes were used for background estimation but only human probes were considered for normalization and summarization phases.
|
| |
|
| Submission date |
Nov 18, 2011 |
| Last update date |
Feb 08, 2012 |
| Contact name |
Stefania Bortoluzzi |
| E-mail(s) |
stefania.bortoluzzi@unipd.it
|
| Phone |
++30 049 827 6502
|
| Organization name |
University of Padova
|
| Department |
Department of Molecular Medicine
|
| Lab |
Computational Genomics
|
| Street address |
via G. Colombo 3
|
| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL14613 |
| Series (1) |
| GSE33809 |
Inhibition of Jak2 in SET2 cell line with INC424 (two time points and 3 dose levels in triplicate) |
|
