|
| Status |
Public on Oct 31, 2015 |
| Title |
HUT78_control_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
HUT78 untreated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HUT78
treatment: control
time: -
|
| Treatment protocol |
Cells were incubated with INCB018424 (using an IC50 concentration) at two times (30 minutes and 3 hours)
|
| Growth protocol |
Cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin (Invitrogen Corporation, USA) in a humidified atmosphere at 37°C with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by Trizol reagent (Invitrogen). RNA quality was checked using total RNA (small fraction chip) with the Agilent 2100 Bioanalyzer (Agilent Technologies) and by 1% agarose electrophoresis, following standard procedures
|
| Label |
Cy3
|
| Label protocol |
Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases.Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores.
|
| |
|
| Channel 2 |
| Source name |
Universal Human Reference RNA Stratagene
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: untreated
|
| Treatment protocol |
Cells were incubated with INCB018424 (using an IC50 concentration) at two times (30 minutes and 3 hours)
|
| Growth protocol |
Cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin (Invitrogen Corporation, USA) in a humidified atmosphere at 37°C with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by Trizol reagent (Invitrogen). RNA quality was checked using total RNA (small fraction chip) with the Agilent 2100 Bioanalyzer (Agilent Technologies) and by 1% agarose electrophoresis, following standard procedures
|
| Label |
Cy5
|
| Label protocol |
Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases.Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores.
|
| |
|
| |
| Hybridization protocol |
Microarray: Human Gene Expression G3 60K (Agilent microarray design ID 028004, P/N G4851A). Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours
|
| Scan protocol |
Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed
|
| Description |
Sample 1
|
| Data processing |
Background correction: normexp; Within arrays normalization: loess; Between arrays normalization: quantiles
|
| |
|
| Submission date |
May 05, 2015 |
| Last update date |
Oct 31, 2015 |
| Contact name |
Nerea Martinez |
| Organization name |
IDIVAL
|
| Lab |
Cancer Genomics
|
| Street address |
Avda Cardenal Herrera Oria
|
| City |
Santander |
| ZIP/Postal code |
E 39011 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16699 |
| Series (1) |
| GSE68562 |
Effect of a JAK inhibitor on gene expression of HUT78 cell line |
|
