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Sample GSM477730 Query DataSets for GSM477730
Status Public on Mar 18, 2010
Title Placenta_Spike_Pool5_Ambion/Affy
Sample type RNA
 
Source name Human Placenta_Spike_Pool5
Organism Homo sapiens
Characteristics tissue: Placenta
gender: Female
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from placental tissue using the miRVana Isolation Kit (Ambion). Protocol was used in such a way that small RNAs were retained.
Label Biotin
Label protocol Samples were processed by Asuragen Services (Austin,TX), according to the company’s standard operating procedures. Briefly, samples were biotinylated and purified using BioSpin6 (Bio-Rad, Hercules CA).
 
Hybridization protocol Hybridization, washing, staining, imaging, and signal extraction were performed according to Affymetrix-recommended procedures, except that the 20X GeneChip Eukaryotic Hybridization Control cocktail was omitted from the hybridization.
Scan protocol Scanned as per Asuragen's standard operating procedures.
Description A0008644.CEL
Data processing Two overlapping probes were designed for each mature miRNA candidate. The staggered probe design provides the flexibility required for probes to capture slight variations in the ends of the processed mature miRNA. For computationally predicted miRNA, this probe design strategy accounts for the uncertainty associated with predicting the precise cleavage site of the processed mature miRNA. The signal processing implemented for the Ambion miRChip is a multi-step process involving probe specific signal detection calls, background estimate and correction, constant variance stabilization and either array scaling or global normalization. For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C-matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization method described by Huber et al. (Huber et al., 2002).
Based on historical performance of the probes on a training data set, each of the two probes is assigned to either A or B bin. Variance Stabilization Normalization (VSN) technique is used to normalize the data. A probes are used for data interpretation.
 
Submission date Dec 01, 2009
Last update date Mar 18, 2010
Contact name Sachin Sah
Organization name Asuragen Inc.
Street address 2150 Woodward St, Suite 100
City Austin
State/province TX
ZIP/Postal code 78744
Country USA
 
Platform ID GPL9735
Series (1)
GSE19248 Performance Evaluation of Commercial miRNA Expression Array Platforms

Data table header descriptions
ID_REF
VALUE VSN normalized signal intensity

Data table
ID_REF VALUE
aga-bantam_st2 2.57473978
aga-let-7_st1 9.522285588
aga-miR-10_st1 8.8223531
aga-miR-124_st1 2.57473978
aga-miR-13b_st1 2.57473978
aga-miR-14_st1 2.982039044
aga-miR-1_st1 4.179736571
aga-miR-210_st1 6.546512026
aga-miR-219_st1 10.60904621
aga-miR-263_st1 5.323233194
aga-miR-275_st2 2.329182827
aga-miR-276_st2 5.077257398
aga-miR-277_st2 2.790623641
aga-miR-278_st2 2.790623641
aga-miR-279_st1 2.982039044
aga-miR-281_st1 2.57473978
aga-miR-282_st1 3.232494159
aga-miR-283_st1 2.57473978
aga-miR-2_st1 2.68604653
aga-miR-305_st1 2.889098232

Total number of rows: 14215

Table truncated, full table size 399 Kbytes.




Supplementary file Size Download File type/resource
GSM477730.CEL.gz 213.0 Kb (ftp)(http) CEL
Processed data included within Sample table

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