MicroRNA and Salmo Salar

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Introduction

GC and SK sent samples to Arraystar, Rockville MD for miRNA analysis. What follows is an attempt to make sense of the results.

outline of pipeline

  • miRNA Expression Profiling
  • Novel miRNA detection
  • Differentially expressed miRNAs
  • miRNA target prediction
  • Pathway Analysis

Excel files in results

We can use this listing to see miRNAs and files of interest

mirRNA Expression Profiling 

./miRNA_Expression_Profiling/All_Comparisons_of_Expressed_miRNAs.xls
./miRNA_Expression_Profiling/miRNA_Expression_Analysis.xls

Novel miRNAs 

./Novel_miRNAs/novel_miRNAs_predicted_by_miRDeep2.xls

Differentially expressed miRNAs 

./Differentially_Expressed_miRNAs/Differentially_Expressed_miRNAs.xls

Initial target prediction 

./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-132-5p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-132-5p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-23b-5p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-23b-5p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-30e-5p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-30e-5p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-8157-3p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-8157-3p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-let-7c-3p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-let-7c-3p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-let-7d-3p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-let-7d-3p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-146a-3p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-146a-3p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-222b-5p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-222b-5p/Target Sites.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-731-3p/Target Genes.xls
./miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-731-3p/Target Sites.xls

Initial pathway Analysis 

./Pathway_Analysis_Results__miRNA_Targets_/Smolt_vs_Parr_down.mature_mirna/sas_pathwayResult.xls
./Pathway_Analysis_Results__miRNA_Targets_/Smolt_vs_Parr_up.mature_mirna/sas_pathwayResult.xls

Supplemental target prediction 

./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-23b-5p/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-23b-5p/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-8157-3p/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-8157-3p/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03020525.1_11615/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03020525.1_11615/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03067625.1_26128/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03067625.1_26128/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03074379.1_27027/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03074379.1_27027/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03101962.1_28818/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_down.mature_mirna/ssa-miR-novel-AGKD03101962.1_28818/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-222b-5p/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-222b-5p/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-731-3p/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-731-3p/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03022511.1_12826/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03022511.1_12826/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03052739.1_23807/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03052739.1_23807/Target Sites.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03052741.1_23813/Target Genes.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/miRNA_Targets_Prediction/Smolt_vs_Parr_up.mature_mirna/ssa-miR-novel-AGKD03052741.1_23813/Target Sites.xls

Supplemental Pathway Analysis 

./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/Pathway Analysis/down.mature_mirna/sas_pathwayResult.xls
./Svetlana Kalujnaia J_053117-miRNA-seq-6 (Supplement) 09282017/Pathway Analysis/up.mature_mirna/sas_pathwayResult.xls

In summary

miRNAs of interest are as follows:

Initial target prediction 

Down-regulated:
ssa-miR-132-5p
ssa-miR-23b-5p
ssa-miR-30e-5p
ssa-miR-8157-3p
Up-regulated:
ssa-let-7c-3p
ssa-let-7d-3p
ssa-miR-146a-3p
ssa-miR-222b-5p
ssa-miR-731-3p

Supplemental target prediction 

Down-regulated:
ssa-miR-23b-5p
ssa-miR-8157-3p
ssa-miR-novel-AGKD03020525.1_11615
ssa-miR-novel-AGKD03067625.1_26128
ssa-miR-novel-AGKD03074379.1_27027
ssa-miR-novel-AGKD03101962.1_28818
Up-regulated:
ssa-miR-222b-5p
ssa-miR-731-3p
ssa-miR-novel-AGKD03022511.1_12826
ssa-miR-novel-AGKD03052739.1_23807
ssa-miR-novel-AGKD03052741.1_23813
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