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Sample GSM2204327 Query DataSets for GSM2204327
Status Public on Feb 27, 2017
Title H2009mock1
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 16.89775741
DarkCorner 5.109721994
A_23_P117082 13.3474085
A_33_P3246448 5.221891563
A_33_P3318220 5.1926035
A_33_P3236322 5.245852133
A_33_P3319925 5.656650088
A_21_P0000509 18.22219009
A_21_P0000744 10.76506812
A_24_P215804 10.00074469
A_23_P110167 12.79392336
A_33_P3211513 8.08385358
A_23_P103349 5.713448723
A_32_P61480 5.434195898
A_33_P3788124 5.14242874
A_33_P3414202 7.660497803
A_33_P3316686 9.374196254
A_33_P3300975 5.434195898
A_33_P3263061 12.16407791
A_33_P3261373 5.434195898

Total number of rows: 50739

Table truncated, full table size 1257 Kbytes.

Supplementary file Size Download File type/resource
GSM2204327_046_MA_1400253949441027_Cy3_501_1_4.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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