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Sample GSM1675618 Query DataSets for GSM1675618
Status Public on Oct 31, 2015
Title HUT78_control_rep3
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 7
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 GPL13607
Series (1)
GSE68562 Effect of a JAK inhibitor on gene expression of HUT78 cell line

Data table header descriptions
ID_REF
VALUE normalized log10 ratio representing test/reference

Data table
ID_REF VALUE
4 -0.347087166
5 -0.034158188
6 -0.391473081
7 0.471258019
8 -0.184415242
9 -0.053802683
10 -0.563619162
11 -0.060339025
12 -0.989625127
13 -0.132550259
14 -0.312634722
15 -0.706191243
16 -0.056827594
17 -0.868329618
18 0.036098429
19 0.258291726
20 -0.495687321
21 0.108253774
24 -0.453384961
25 1.889813093

Total number of rows: 58717

Table truncated, full table size 1048 Kbytes.




Supplementary file Size Download File type/resource
GSM1675618_US22502553_252800418069_S01_GE2_1105_Oct12_B_1_1.txt.gz 6.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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