Transcriptomics Plants Workflow

PMI Workflow – Transcriptomics Plants  

Transcriptomics in the PMI involves precise measurements of RNA content in eukaryotic (plant or yeast) or prokaryotic (bacterial) cells    

Step 1 Experiment Information

This step includes general information about source of bacterial isolates, PI, experimenter, technician etc.

    Entered Date:
    Experiment Name:
    Associated PIs:
    Origin and date of bacterial isolate:
    Comments:   Any extra information as required
    File: Upload Date

Step 2:  RNA Isolation

Extracting RNA from plant tissue.

NCBI Organism Id Number Cell or Tissue type Treatment – (Textarea)
Sample Ids – (Textarea)                  
RNA Isolation Protocol  (text window)
RNA Quantity/Quality Control (Textarea)
RNA QC File Upload (File Upload)

Step 3: RNA-seq Library Prep

Creating sequence libraries.                    

RNA-seq Library Prep – (Textarea)
Library Prep Quantity/Quality Control (Textarea)
Library Prep QC File Upload (File Upload)
Sample Barcodes – (Textarea)

Step 4:  Sequencing                  

Generating sequencing reads.                    

Device Used (Pick – MiSEQ, HiSEQ)
Sequencing Kit – (Textarea)
Result fastQ/raw files (File Upload)

Step 5:  Data Cleaning

Removing low quality reads, sequencing adapters and contaminating sequences from plant plastids and mitochondria genomes.

Trimming Protocol – (Textarea)
Trimming Low Quality Reads (File Upload)
Filtering Protocol – (Textarea)
Link to Contamination Database – (Text Field)
Filtering Contaminating Reads (File Upload)                  

Step 6:  Transcript Assembly and Quantitative Analysis

Depending on the availability of the reference genome, we are using mapping-based or de novo approaches to assemble transcript, estimate their abundances and test for differential expressions.

Software Used (chose from a pick list – CUFFLINKS, TRINITY)
Bash Script (File Upload)
Reference Genome Upload (File Upload)
Result File Upload (File Upload)