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Sample GSM477731 Query DataSets for GSM477731
Status Public on Mar 18, 2010
Title Placenta_Spike_Pool6_Ambion/Affy
Sample type RNA
Source name Human Placenta_Spike_Pool6
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 A0008645.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
VALUE VSN normalized signal intensity

Data table
aga-bantam_st2 2.416294111
aga-let-7_st1 9.532452259
aga-miR-10_st1 8.687729997
aga-miR-124_st1 2.644917274
aga-miR-13b_st1 3.027487919
aga-miR-14_st1 2.416294111
aga-miR-1_st1 4.710660835
aga-miR-210_st1 7.271399781
aga-miR-219_st1 9.530465239
aga-miR-263_st1 3.189726393
aga-miR-275_st2 1.159660464
aga-miR-276_st2 4.330013165
aga-miR-277_st2 2.416294111
aga-miR-278_st2 3.709021844
aga-miR-279_st1 2.416294111
aga-miR-281_st1 2.644917274
aga-miR-282_st1 2.15611688
aga-miR-283_st1 3.027487919
aga-miR-2_st1 2.416294111
aga-miR-305_st1 4.330013165

Total number of rows: 14215

Table truncated, full table size 401 Kbytes.

Supplementary file Size Download File type/resource
GSM477731.CEL.gz 213.4 Kb (ftp)(http) CEL
Processed data included within Sample table

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