NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1174479 Query DataSets for GSM1174479
Status Public on Jun 27, 2013
Title caffeine- 3
Sample type RNA
 
Source name granulocytes not treated with caffeine
Organism Mus musculus
Characteristics strain: C57BL/6J
cell type: granulocytes
Treatment protocol Cells were plated at a density of 3x105 cells per ml in two different tissue culture plates. The optimal concentration of caffeine (15 mM) was added to the culture medium for 4 hours before cells were washed twice with PBS. Actinomycin D (2 μg/ml) together with caffeine was then added into one plate whereas only actinomycin D was added to the other to block transcription of genes. After an additional 4 hours incubation, total RNA was collected and used for microarray analysis.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Biotin
Label protocol Biotinylated cDNA were prepared according to the Encore Biotin Module (Nugen) from 300 ng total RNA.
 
Hybridization protocol Following fragmentation, samples were injected into Affymetrix array chips and hybridized at 45°C and 60 rpm for 17 hours in a hybridization oven (Affymetrix). GeneChips were stained and washed in the Affymetrix GeneChip Fluidic Station 450
Scan protocol GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G
Data processing The data was analysed using R with the RUV procedure described in http://statistics.berkeley.edu/tech-reports/800 for scaling and normalization.
 
Submission date Jun 26, 2013
Last update date Jun 27, 2013
Contact name william ritchie
Organization name centenary institute
Street address Building 93
City Camperdown
State/province NSW
ZIP/Postal code 2050
Country Australia
 
Platform ID GPL6246
Series (2)
GSE48306 Orchestrated intron retention regulates normal granulocyte differentiation [Affymetrix arrays]
GSE48307 Orchestrated intron retention regulates normal granulocyte differentiation

Data table header descriptions
ID_REF
VALUE log-transformed RUV normalized signal intensity

Data table
ID_REF VALUE
10338001 12.50195275
10338003 11.01230026
10338004 10.06652642
10338017 13.13021358
10338025 9.601162766
10338026 13.44624313
10338029 10.0408663
10338035 9.813171185
10338036 9.967405103
10338037 3.98168235
10338041 11.5286964
10338042 10.88133801
10338044 12.6232247
10338047 5.854004639
10338056 3.736901508
10338059 13.47399248
10338060 3.957835837
10338063 4.06133188
10338064 5.265403094
10338065 5.277053176

Total number of rows: 34760

Table truncated, full table size 709 Kbytes.




Supplementary file Size Download File type/resource
GSM1174479_GeneT_JustinW_20110531_6.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap