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Sample GSM662808 Query DataSets for GSM662808
Status Public on Jun 15, 2011
Title Variant 1 pool rep2
Sample type other
 
Source name Synthetic oligo pool
Organism synthetic construct
Characteristics assay: variant 1
Extracted molecule other
Extraction protocol Synthetic oligos were synethesized by IDT and Qiagen. We assayed three pools of synthetic RNA oligonucleotides representing canonical, variant 1, and variant 2 versions of 5 miRNAs (miR-15a, miR-15b, miR-125a-5p, miR-143 and miR-221), with each miRNA at a concentration of 30 pmol. We also assayed a mixed pool containing 60% canonical, 30% Variant 1, and 10% Variant 2 for each of the 5 miRNAs listed above.
Label N/A
Label protocol N/A
 
Hybridization protocol Hybrdization reactions were performed according to the manufacturer's instructions (NanoString) with 5 µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.
Scan protocol Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions. For each assay, a high-density scan (600 fields of view) was performed.
Description Replicate 2
Data processing The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls. The sum of the positive controls for a given sample was divided by the mean sum of the positive controls across all samples to yield a normalization factor. Multiplication of this normalization factor by the raw counts yielded normalized counts.
 
Submission date Jan 27, 2011
Last update date Jun 15, 2011
Contact name Muneesh Tewari
E-mail(s) mtewari@fhcrc.org
Organization name Fred Hutchinson Cancer Research Center
Department Human Biology
Lab Tewari
Street address 1100 Fairview Ave, N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL11668
Series (2)
GSE26916 Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (Validation 1)
GSE26970 Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity

Data table header descriptions
ID_REF
VALUE normalized miRNA counts

Data table
ID_REF VALUE
1 55
2 269
3 27
4 185
5 177
6 11726
7 11925
8 10117
9 2467
10 10951
11 838
12 73
13 53
14 60
15 108

Total number of rows: 15


Supplementary data files not provided
Processed data included within Sample table

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