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And for the small ones, the normalized formula is: a_{ij} = frac{{mathop {hbox{max} }limits_{j} left{ {r_{ij} } right} - r_{ij} }}{{mathop {hbox{max} }limits_{j} left{ {r_{ij} } right} - mathop {hbox{min} }limits_{j} left{ {r_{ij} } right}}} (8).
In terms of the index of excellence, the normalized formula is: a_{ij} = frac{{r_{ij} - mathop {hbox{min} }limits_{j} left{ {r_{ij} } right}}}{{mathop {hbox{max} }limits_{j} left{ {r_{ij} } right} - mathop {hbox{min} }limits_{j} left{ {r_{ij} } right}}} (7).
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Then the sRNAs counts and miRNA IDs of every line were obtained and all the counts were normalized according to the normalization formula (Normalized expression = Actual miRNA count/Total count of clean reads*15,000,000).
Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000; (2) Calculate fold-change and P-value from the normalized expression.
The readcounts of miRNAs were transformed into TPM (transcript per million) through the following criteria: Normalization formula: Normalized expression = (mapped readcount/Total reads)*1000000 [ 48] and then analyzed the abundance of miRNAs.
The clean reads from each miRNA were normalized using the following formula: Normalized expression = mapped readcount/Total reads*1000000.
As a secondary validation analysis using SOAP [ 31], count data was individually normalized across 8 libraries using the formula: normalized expression (NE) = actual miRNA count/total count of clean reads × 10 using SOAP.
To compare the miRNA expression between two libraries to find out the differentially expressed miRNAs, the expression of miRNA in two libraries (big-size group and small-size group) were normalized to obtain the expression of transcripts per million using the following formula: Normalized expression = (Actual miRNA count/Total count of clean reads)*1,000,000.
To analyze differential miRNA, miRNAs expression in each library (42-d and 162-d chicken ovary) was normalized to obtain the expression of transcripts per million using the following formula: Normalized expression = (Actual miRNA sequencing reads count / Total clean reads count) × 1,000,000.
Then, the fold-change and P-value were calculated from the normalized expression using the formula.
Normalized expression was calculated by formula:{(EfficiencyhANT4) CT hANT4/ (EffiCTencyALG9} CT ALG9} using qGene software [31].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com