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Sample GSM552146 Query DataSets for GSM552146
Status Public on Jun 09, 2010
Title HeLa, siRNA, fdxr-3, 0.5nM, 24hr
Sample type RNA
 
Source name Hela cells
Organism Homo sapiens
Characteristics cell line: Hela cells
conditions: siRNA, fdxr-3, 0.5nM, 24hr
Extracted molecule total RNA
Extraction protocol Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
Label Biotin
Label protocol The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.
 
Hybridization protocol GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45?C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.
Scan protocol Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.
Description Affymetrix Hela profiling of siRNA/shRNA treatments
Data processing Data were loaded into the Rosetta ResolverĀ® system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260). Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value. The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://0-bioinformatics-oxfordjournals-org.brum.beds.ac.uk/cgi/content/full/22/9/1111).
 
Submission date Jun 07, 2010
Last update date Jun 08, 2010
Contact name Michele Cleary
E-mail(s) michele_cleary@merck.com
Phone 215 652-6104
Organization name Merck and Co., Inc.
Department Genetics and Pharmacogenomics
Lab Target & Pathway Biology
Street address 770 Sumneytown Pike
City West Point
State/province PA
ZIP/Postal code 19486
Country USA
 
Platform ID GPL10379
Series (1)
GSE22209 Reduced seed region-based off-target activity with lentivirus-mediated RNAi

Data table header descriptions
ID_REF Rosetta generated unique probe identifier
VALUE Expression level
DETECTION P-VALUE P-value of expression level

Data table
ID_REF VALUE DETECTION P-VALUE
merck-N79601_RC_at 96.9732 5.8594e-003
merck-AK128290_at 4.1121 4.3237e-001
merck-NC_001526_ORF_1178_at 6.1044 2.1948e-001
merck-NC_001526_ORF_1179_at 3.5331 7.2583e-001
merck-NC_001526_ORF_1180_at 3.2867 6.3379e-001
merck-NC_001526_ORF_1181_s_at 11.2081 6.6553e-001
merck-NC_001526_ORF_1182_at 4.0675 6.6553e-001
merck-NC_001357_ORF_1183_at 816.9385 2.4414e-004
merck-NC_001357_ORF_1184_at 178.7147 2.4414e-004
merck-NC_001357_ORF_1185_at 5.2884 6.6553e-001
merck-NC_001357_ORF_1186_at 4.5364 2.1948e-001
merck-NC_001357_ORF_1187_a_at 3421.8154 2.4414e-004
merck-NC_001357_ORF_1188_a_at 5377.1885 2.4414e-004
merck-NC_001357_ORF_1189_s_at 8.9268 9.6045e-001
merck-NC_001357_ORF_1190_at 11.7191 8.0542e-001
merck-X04370_ORF_1249_s_at 15.2637 3.3447e-001
merck-X04370_ORF_1258_s_at 6.7561 7.5391e-001
merck-X04370_ORF_1261_s_at 3.6478 9.4385e-001
merck-NC_001526_ORF_1177_at 5.8135 5.6152e-002
merck-NC_001545_ORF_1341_at 12.5612 9.9927e-001

Total number of rows: 52378

Table truncated, full table size 1908 Kbytes.




Supplementary file Size Download File type/resource
GSM552146.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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