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Sample GSM2204329 Query DataSets for GSM2204329
Status Public on Feb 27, 2017
Title H2009mock3
Sample type RNA
Source name NSCLC cell line H2009, mock
Organism Homo sapiens
Characteristics cell line: H2009
cell type: non-small cell lung cancer (NSCLC) cell line
plasmid: empty vector
Treatment protocol wtB2M cells were infected with a plasmid carrying B2M gene; mock cells correspond to the infection with the empty vector.
Growth protocol Cells grown in HITES with 5% FBS.
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 Low Input QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).
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 manufacturer's 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.
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 17, 2016
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 (1)
GSE83490 Identification of expression patterns after B2M restoration in deficient lung cancer cell lines
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 16.744561
DarkCorner 5.013613949
A_23_P117082 13.27959354
A_33_P3246448 5.984597886
A_33_P3318220 5.186013501
A_33_P3236322 5.378929157
A_33_P3319925 5.78756414
A_21_P0000509 18.11180719
A_21_P0000744 10.75835124
A_24_P215804 10.73212109
A_23_P110167 12.72917342
A_33_P3211513 7.98671644
A_23_P103349 5.581206803
A_32_P61480 5.491437582
A_33_P3788124 5.507383692
A_33_P3414202 7.671891597
A_33_P3316686 9.316912124
A_33_P3300975 5.512660134
A_33_P3263061 12.43389715
A_33_P3261373 5.626547421

Total number of rows: 50739

Table truncated, full table size 1258 Kbytes.

Supplementary file Size Download File type/resource
GSM2204329_048_MA_2200253949437762_Cy3_503_2_2.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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