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Sample GSM454301 Query DataSets for GSM454301
Status Public on Feb 08, 2011
Title NME2 Control A549 cell Replicate1
Sample type RNA
 
Source name Control A549
Organism Homo sapiens
Characteristics tissue type: lung adenocarcinoma
cell line: A549
Extracted molecule total RNA
Extraction protocol Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). In brief, total RNA was initially isolated using TRI Reagent (Sigma, St. Louis, MO), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up. All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA present in the isolated total RNA (5 ug total RNA starting material each sample reaction) using the one cycle cDNA synthesis kit (Affymetrix, Inc.,Santa Clara CA ). A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the Gene Chip IVT labeling kit.20ug of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).
 
Hybridization protocol Subsequently, 15 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HU133 plus 2.0 array.
Scan protocol The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip Scanner 3000.
Description NME2
Data processing The results were quantified and analyzed using GCOS 1.1.1 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).
 
Submission date Sep 18, 2009
Last update date Feb 08, 2011
Contact name Vinod Kumar Yadav
E-mail(s) vinod.yadav@igib.in
Organization name IGIB
Department Bioinformatics
Street address Mall Road
City Delhi
State/province Delhi
ZIP/Postal code 110009
Country India
 
Platform ID GPL570
Series (2)
GSE18182 Expression profile of lung adenocarcinoma, A549 cells following targeted depletion of non metastatic 2 (NME2/NM23 H2)
GSE18285 Characterization of the transcriptional roles of NME2

Data table header descriptions
ID_REF
VALUE MAS 5.0 Signal
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 492 P 0.000662
AFFX-BioB-M_at 782 P 0.00007
AFFX-BioB-3_at 451.7 P 0.000195
AFFX-BioC-5_at 1314.2 P 0.000095
AFFX-BioC-3_at 1929.2 P 0.000044
AFFX-BioDn-5_at 2957.3 P 0.000044
AFFX-BioDn-3_at 5684.8 P 0.000147
AFFX-CreX-5_at 13881.5 P 0.000052
AFFX-CreX-3_at 16440 P 0.000044
AFFX-DapX-5_at 95 P 0.000169
AFFX-DapX-M_at 454.2 P 0.002275
AFFX-DapX-3_at 816.9 P 0.000095
AFFX-LysX-5_at 32.2 P 0.01254
AFFX-LysX-M_at 108.3 A 0.083592
AFFX-LysX-3_at 282.2 P 0.000297
AFFX-PheX-5_at 38.3 P 0.01667
AFFX-PheX-M_at 63.5 A 0.0727
AFFX-PheX-3_at 137.6 P 0.00762
AFFX-ThrX-5_at 35.3 A 0.262827
AFFX-ThrX-M_at 93.4 P 0.004017

Total number of rows: 54675

Table truncated, full table size 1435 Kbytes.




Supplementary file Size Download File type/resource
GSM454301.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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