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Sample GSM1617939 Query DataSets for GSM1617939
Status Public on Sep 08, 2016
Title DMS114_COMB_3
Sample type RNA
 
Source name Lung
Organism Homo sapiens
Characteristics individual: Diseased donor
cell line: SCLC cell line DMS114
cell line type: BRG1 mutant
treatment: COMB
Treatment protocol GCRA: Dexamethasone (1uM) + Retinoic Acid (1uM) 120hours; COMB: Dexamethasone (1uM) + Retinoic Acid (1uM) + Aza (0.2uM) + SAHA (0.2uM) 120 hours
Growth protocol Cells where growth on RPMI media with 10% FBS, 1% PS
Extracted molecule total RNA
Extraction protocol Total RNA were extracted using Trizol Reagent.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 45ng total RNA using a LowInput QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C 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), then dried immediately by brief centrifugation.
Scan protocol Scanner Agilent G2565CA Feature extraction 10.7
Description Sample name: DMS114_P_COMB_4033
Cancer cell line
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Feb 24, 2015
Last update date Apr 23, 2018
Contact name Manel Esteller
Organization name IDIBELL
Department PEBC
Lab Cancer Epigenetics
Street address Hospital Duran i Reynals Av. Gran Via s/n km, 2.7
City L'Hospitalet de Llobregat
State/province Barcelona
ZIP/Postal code 08908
Country Spain
 
Platform ID GPL17077
Series (2)
GSE66244 Identification of expresion patterns after treatment with GC/RA and combination with AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines
GSE66245 Treatment with GC/RA and combination with AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 16.13344746
DarkCorner 4.312843331
A_23_P117082 13.97396319
A_33_P3246448 5.017525013
A_33_P3318220 4.751512662
A_33_P3236322 4.751512662
A_33_P3319925 5.382915301
A_21_P0000509 17.22256809
A_21_P0000744 10.36481591
A_24_P215804 9.60276595
A_23_P110167 5.640653604
A_33_P3211513 8.168557117
A_23_P103349 5.431657534
A_32_P61480 4.875976184
A_33_P3788124 5.363295059
A_33_P3414202 6.286910882
A_33_P3316686 8.089581786
A_33_P3300975 10.82826617
A_33_P3263061 11.09375053
A_33_P3261373 4.688319559

Total number of rows: 50739

Table truncated, full table size 1258 Kbytes.




Supplementary file Size Download File type/resource
GSM1617939_463_NA_1400253949431325_Cy3_4033_1_4.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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