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Sample GSM1617900 Query DataSets for GSM1617900
Status Public on Sep 08, 2016
Title H82_shBRG1_GCRA_3
Sample type RNA
 
Source name Lung
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 Sample name: H82_Sh_GC_RA_1223
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 16.19672987
DarkCorner 4.55564155
A_23_P117082 11.4734941
A_33_P3246448 7.248011812
A_33_P3318220 4.081519457
A_33_P3236322 4.657474453
A_33_P3319925 5.23579551
A_21_P0000509 17.57450571
A_21_P0000744 10.21463899
A_24_P215804 8.454242344
A_23_P110167 10.03221291
A_33_P3211513 9.42569231
A_23_P103349 5.840693464
A_32_P61480 4.629668565
A_33_P3788124 4.494838167
A_33_P3414202 8.006108105
A_33_P3316686 8.707923079
A_33_P3300975 11.49075507
A_33_P3263061 11.01266248
A_33_P3261373 4.79845322

Total number of rows: 50739

Table truncated, full table size 1259 Kbytes.




Supplementary file Size Download File type/resource
GSM1617900_421_NA_1300253949431325_Cy3_1223_1_3.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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