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The length distribution of the clean total reads and unique reads were then summarized.
Adaptors, low-quality tags and contaminants were removed from raw reads produced by Solexa sequencing to produce the clean total reads.
The data showed a greater number of unique reads per unit value of the clean total reads in the NaCl-treated library than in the control library.
Adaptor removal and filtering of the < 16 nt and > 30 nt data, t/rRNA matches, etc. yielded 8981591 and 7923122 clean total reads in the control and NaCl-treated libraries, respectively, and they could be putative miRNAs and/or siRNAs.
cDNA was generated from 300 ng of clean total RNA from all samples using the Superscript III First Strand Synthesis System Kit (Invitrogen) following the manufacturer's instructions with random hexamer primers and a RNaseH treatment step.
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Cleaned total RNA was converted to cDNA with the ThermoScript RT/PCR System (Invitrogen) using oligo dT) primers.
Each one of the 32 individuals contributed an equal quantity of cleaned total RNA (HK = 10 μg; L = 8 μg; M = 10 μg) to each tissue/treatment group-specific pool.
Two and a half μg of cleaned total RNA were reverse transcribed using Superscript II enzyme (Invitrogen, France) with Oligo dT) primers (Invitrogen, France) and cDNAs were quantified with the 2100 Bioanalyzer (Agilent Technologies, France) and diluted to obtain a 30 ng/μl final concentration for all samples.
For each one of the tissues used for library construction [head kidney (HK), liver (L) and skeletal muscle (M ] DNase-I treated, column-cleaned total RNA samples from the CT and HS groups taken at sampling times CS, 3ACS, 12ACS, and 24ACS were pooled for mRNA isolation (n = 32 for each group within each tissue).
2 mg cleaned total RNA from each of the four samples, semigametic anthers and ovules as well as non-semigametic anthers and ovules, and Affymetrix GeneChips© Cotton Genome Array (Santa Clara, CA) were sent to Genome Explorations (Memphis, TN) for hybridization and preliminary data analysis.
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