GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2198063 Query DataSets for GSM2198063
Status Public on Dec 16, 2016
Title PT1 CD36-#4
Sample type RNA
Source name PT1 CD36-
Organism Homo sapiens
Characteristics group: PT1
cd36 population: CD36- 286.29
Growth protocol Cells were grown in an orthotopic xenograft model in NOD-SCIDγ mice (NSG)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from FACS sorted cells with RNAClean XP kit– Agentcourt A63987 following the manufacturer’s instructions and immediately amplified using the TransPlex Complete Whole Transcriptome Amplification Kit (Sigma WTA2) to generate the cDNA
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cDNA was prepared from 500ng of ds cDNA using the SureTag Complete DNA Labeling kit (Agilent 5190-4240) according to manufacturer’s instructions. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectophotometer.
Hybridization protocol 600ng of Cy3 labeled cDNA was directly mix with hybridization buffer and Agilent blocking agent incubated at 95ºC for 3 minutes and immediately transfer on ice. Then, it was hybridized on microarrays for 40h at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)
Scan protocol The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
Description 772 2016
Data processing Background correction was applied with normexp method and offset=45. Quantile normalization followed by avereps to average over replicate probes. All functions from the R limma package
Submission date Jun 13, 2016
Last update date Dec 16, 2016
Contact name Antoni Berenguer-LLergo
Organization name Parc Taulí Research and Innovation Institute (I3PT)
Department A8G2 Group - Rheumatology Service
Street address Parc del Taulí, 1
City Sabadell
State/province Barcelona
ZIP/Postal code 08208
Country Spain
Platform ID GPL17077
Series (1)
GSE83276 Targeting metastasis stem cells through the fatty acid receptor CD36

Data table header descriptions
VALUE log2 expression values

Data table
GE_BrightCorner 15.181367
DarkCorner 5.971433738
A_23_P117082 10.82053014
A_33_P3246448 6.64758036
A_33_P3318220 6.420912677
A_33_P3236322 13.11119663
A_33_P3319925 6.885330458
A_21_P0000509 9.279987326
A_21_P0000744 8.230430705
A_24_P215804 9.67111372
A_23_P110167 11.9851379
A_33_P3211513 13.46411234
A_23_P103349 8.736116393
A_32_P61480 5.918606688
A_33_P3788124 6.132624536
A_33_P3414202 13.18195688
A_33_P3316686 10.15784344
A_33_P3300975 10.45598788
A_33_P3263061 10.94022098
A_33_P3261373 7.053495819

Total number of rows: 50739

Table truncated, full table size 1258 Kbytes.

Supplementary file Size Download File type/resource
GSM2198063_146_NA_1400253949445874_Cy3_772_2016_1_4.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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