RNA-Sequencing Analysis of Heinz 1706 Genome Meristem and Leaf Tissue Samples

Graphical abstract showing workflow of project. Workflow as follows: 1. tomato plant with meristem and leaf highlighted with text "tissue collection. 2. sample tube with text "RNA extraction and cDNA library preparation. 3. illumina instrument with text "NGS". 4. barcode and sequencing read with text "indexing and alignment". 5. file icon with text "quantification" 6. graph icon with text "data exploration

Project Investigation

The purpose of this project was to analyze RNA-seq data sets from the crop Solanacea lycopersicm. I studied changes in tomato gene expression between apical meristem and leaf samples when sequenced at a depth of 3X and aligned to the reference genome Heinz 1706 version 5.0 Tomato. This genome was sequences using PacBio HIFi. This was the first ever tomato genome assembled.

Quality Control: FastQC

FastQC was preformed to do quality control checks on raw sequence data from NGS.

Indexing and Alignment

Reference genome was indexed and sequenced reads were aligned to genome.

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Quantification

Aligned sequences were quantified into counts to be analyzed downstream.

Data Exploration

Data outputs were explored using a free graphical use

Acknowledgments

I would like to ackowledge the CPT learning community, my research teamares, instructors, and NC State HPC and bioinformatice resources for making this work possible.

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