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Sample GSM2196113 Query DataSets for GSM2196113
Status Public on Sep 08, 2016
Title H82_shBRG1_2_GCRA_2
Sample type RNA
 
Source name Small Cell Lung Cancer (SCLC)
Organism Homo sapiens
Characteristics individual: Diseased donor
cell line: SCLC cell line H82
cell line type: MYC amplified
treatment: shBRG1_GCRA
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 M0102_2016_MA__1100257236312224__Cy3_1322_1_1
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 Jun 09, 2016
Last update date Sep 08, 2016
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 GPL21185
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

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 16.49136247
DarkCorner 5.038824259
A_21_P0014386 7.430169911
A_33_P3396872 5.662281823
A_33_P3267760 6.618968893
A_32_P194264 8.288642342
A_23_P153745 11.41306555
A_33_P3352837 5.45252091
A_21_P0011260 5.236550119
A_33_P3235816 5.539935239
A_21_P0014180 6.062824609
A_24_P944991 6.145468329
A_21_P0006507 5.191974895
A_23_P208706 12.09772219
A_33_P3388806 4.966260926
A_33_P3324839 6.525337062
A_24_P333494 10.42348212
A_22_P00006274 6.062824609
A_23_P161615 9.110510261
A_33_P3384958 7.783451086

Total number of rows: 58341

Table truncated, full table size 1463 Kbytes.




Supplementary file Size Download File type/resource
GSM2196113_M0102_2016_MA_1100257236312224_Cy3_1322_1_1.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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