PSI-Seq

PSI-Seq (Pseudouridine Site Identification Sequencing) is a high-throughput sequencing method used to identify and map pseudouridine (?) modifications in RNA at a transcriptome-wide level.

Pseudouridine is the most abundant RNA modification, commonly found in tRNA, rRNA, and increasingly recognized in mRNA. Unlike uridine, pseudouridine has a C–C glycosidic bond, which affects RNA stability and function.Sites where reverse transcription drops off or terminates significantly more in +CMC than in -CMC indicate pseudouridine sites.The reads are aligned, and termination frequency at each site is compared.

By the end of this course, participants will confidently navigate Linux-based bioinformatics environments and proficiently retrieve, preprocess, and perform quality control on PSI-Seq data. They'll understand the chemistry behind CMCT-mediated pseudouridine detection and will be able to align sequencing reads, visualize RT-stop events in IGV, and calculate pseudouridylation scores at single-nucleotide resolution. Furthermore, learners will harness R to analyze and visualize data, perform functional enrichment.

👉 Enroll now and take the first step toward a future in data-driven biology and beyond.

## 10% Discount if you register before 15th October, 2025. Hurry up!!

RNASeq [R]
RNASeq [D]
scRNA-Seq
lncRNA-Seq
miRNA-Seq
PSI-Seq
ChipSeq
ATAC-Seq
scATA-Seq
Spatial Transcriptome
DNASeq
MethylSeq
Whole Genome de novo Assembly
Targeted metagenomics
Whole Genome Metagenomics
Metatranscriptomics
RAD-Seq
SNAP-ChIP

7 Days Training
15 Days Training

Course Information
Course	PSI-Seq Data Analysis
Duration	online 7 Days Training [ 2 Hours Daily [ Monday To Friday ] ]
Slots	Our working Time is 9:00 AM to 6:00 PM Indian Time Available slots - 9:00 AM to 11:00 AM / 11:00 AM to 1:00 PM / 2:00 PM to 4:00 PM / 4:00 PM to 6:00 PM For training slots after 6 PM or before 9 am as well as weekends training kindly mention during registration accordingly it will be scheduled.
Mode	👉 For online training candidate have to install ZOOM (with remote control on candidate system which makes 100% interactive) 👉 Run time video recording candidate can make as well as pdf manual will be provided for future reference. 👉 All our training is 100% practical and 100% industrial and 100% interactive which provides same as offline learning. 👉 For doubt clear there will be extra support will be provided based on the requirement. 👉 Certificate will be provided
Sequencing Platform	Illumina /Ion Torrent/PacBio/Nanopore
Raw data	Candidate can include maximum 4 datasets of their own during training. Publication standards figures and tables will be generated.
Training Fees
Module-NGS PSI-Seq Data Analysis	📘 Introduction to Bioinformatics & NGS - Bioinformatics fundamentals - NGS platforms (Illumina, Nanopore, etc.) - Omics data overview - Workflow and Algorithm for PSI-Seq 📘 Linux Basics & NGS Tool Installation - Linux terminal & basic commands - Installing bioinformatics tools with conda & apt Tools: FastQC, fastp, Bowtie2, Samtools 📘 Data Retrieval & NGS Data Types - Download data from NCBI SRA OR EBI SRA database - Understand file formats: FASTQ, SAM, BAM, GFF 📘 Pseudouridine Site Detection (CMCT Chemistry) - CMCT modification & reverse transcription stalling - +CMC vs -CMC controls 📘 Read Quality Control - Assess read quality using FastQC - Trim adapters and low-quality bases 📘 Read Alignment to Reference Genome - Align reads - Post-process with Samtools 📘 Read Visualization - Use IGV to inspect BAM files and visualize RT stop sites 📘 Single Nucleotide Metrics - Use bam-readcount to extract per-base coverage and mismatches 📘 R Programming Basics - Vectors, data frames, plotting - Packages: ggplot2, dplyr 📘 Site Scoring - Calculate pseudouridylation score from CMC-treated reads - Normalize +CMC vs -CMC signal 📘 Downstream Analysis of Sites - Differential calculation - Gene annotation - GO and KEGG enrichment 📘 Visualization of Sites - Heatmaps, h-plots, scatter plots - Advanced plotting with R 📘 16: Network & Pathway Analysis - Use STRING-DB for PPI data - Visualize networks in Cytoscape
Preparation	- NCBI : https://pmc.ncbi.nlm.nih.gov/articles/PMC9997552/
Instructor	Industry Experienced
Target Audiance	This course is designed for graduate students, postdoctoral researchers, and professionals working in the fields of conservation biology, evolutionary genomics, and population genetics or any life sciences who are interested in applying genomic tools to real-world conservation challenges.
Contact	Please write us at info@arraygen.com or call or whatsapp us on mobile +91-9673625446 if you need any clarification or for any custom training based on candidate reference paper or candidate own content/tools.

Course Information
Course	PSI-Seq Data Analysis
Duration	online 15 Days Training [ 2 Hours Daily [ Monday To Friday ] ]
Slots	Our working Time is 9:00 AM to 6:00 PM Indian Time Available slots - 9:00 AM to 11:00 AM / 11:00 AM to 1:00 PM / 2:00 PM to 4:00 PM / 4:00 PM to 6:00 PM For training slots after 6 PM or before 9 am as well as weekends training kindly mention during registration accordingly it will be scheduled.
Mode	👉 For online training candidate have to install ZOOM (with remote control on candidate system which makes 100% interactive) 👉 Run time video recording candidate can make as well as pdf manual will be provided for future reference. 👉 All our training is 100% practical and 100% industrial and 100% interactive which provides same as offline learning. 👉 For doubt clear there will be extra support will be provided based on the requirement. 👉 Certificate will be provided
Sequencing Platform	Illumina /Ion Torrent/PacBio/Nanopore
Raw data	Candidate can include maximum 4 datasets of their own during training. Publication standards figures and tables will be generated.
Training Fees
Module-I	Advanced Bioinformatics & basic programming
Topics	📘 Introduction to Bioinformatics - Overview of bioinformatics and its applications - Key concepts in computational biology - Role of bioinformatics in genomics, transcriptomics, and proteomics 📘 Understanding NGS and Genomics Bioinformatics - Basics of Next-Generation Sequencing (NGS) - Types of NGS data (RNA-seq, WGS, WES) - Overview of NGS data formats: FASTQ, BAM, VCF - Introduction to pipelines and tools for NGS data analysis 📘 Databases & Data Retrieval (NCBI and UCSC) - Learning how to retrieve biologically correct data - Performing complete batch retrieval (e.g., whole exome) - NCBI: understanding gene-level data retrieval - UCSC: handling large-scale data retrieval - UCSC Genome Browser and Table Browser usage - Batch Coordinate Retrieval and Genomic Data downloads - GFF/GTF gene annotation formats and how to retrieve them - Using BLAT for sequence-based search and alignment 📘 Gene Prediction and Functional Annotation - Gene prediction approaches and tools - Functional annotation using Gene Ontology (GO) - Pathway analysis using KEGG, Reactome - Interpreting gene sets and biological relevance 📘 Standalone/Offline BLAST for Large-Scale Genomic Data - Installing and setting up standalone BLAST - Running local BLAST for batch sequence alignment - Applications in genome-wide homology searches - Custom BLAST databases and performance optimization 📘 PCR Primer Designing and Specificity Check - Designing accurate primers for PCR amplification - Tools: Primer3, NCBI Primer-BLAST - Checking primer specificity using genome-wide BLAST - Avoiding non-target amplification through design best practices 📘 Understanding Python Programming - Introduction to Python for bioinformatics - Scripting basics: variables, loops, functions - Libraries like Biopython, pandas for biological data handling - Automating genomic workflows with Python scripts
AND
Module-II	Next Generation Sequencing (NGS) - PSI-Seq Data Analysis
Topics	📘 Introduction to Bioinformatics & NGS - Bioinformatics fundamentals - NGS platforms (Illumina, Nanopore, etc.) - Omics data overview - Workflow and Algorithm for PSI-Seq 📘 Linux Basics & NGS Tool Installation - Linux terminal & basic commands - Installing bioinformatics tools with conda & apt Tools: FastQC, fastp, Bowtie2, Samtools 📘 Data Retrieval & NGS Data Types - Download data from NCBI SRA OR EBI SRA database - Understand file formats: FASTQ, SAM, BAM, GFF 📘 Pseudouridine Site Detection (CMCT Chemistry) - CMCT modification & reverse transcription stalling - +CMC vs -CMC controls 📘 Read Quality Control - Assess read quality using FastQC - Trim adapters and low-quality bases 📘 Read Alignment to Reference Genome - Align reads - Post-process with Samtools 📘 Read Visualization - Use IGV to inspect BAM files and visualize RT stop sites 📘 Single Nucleotide Metrics - Use bam-readcount to extract per-base coverage and mismatches 📘 R Programming Basics - Vectors, data frames, plotting - Packages: ggplot2, dplyr 📘 Site Scoring - Calculate pseudouridylation score from CMC-treated reads - Normalize +CMC vs -CMC signal 📘 Downstream Analysis of Sites - Differential calculation - Gene annotation - GO and KEGG enrichment 📘 Visualization of Sites - Heatmaps, h-plots, scatter plots - Advanced plotting with R 📘 16: Network & Pathway Analysis - Use STRING-DB for PPI data - Visualize networks in Cytoscape
Preparation	- NCBI : https://pmc.ncbi.nlm.nih.gov/articles/PMC9997552/
Instructor	Industry Experienced
Target Audiance	This course is designed for graduate students, postdoctoral researchers, and professionals working in the fields of conservation biology, evolutionary genomics, and population genetics or any life sciences who are interested in applying genomic tools to real-world conservation challenges.
Contact	Please write us at info@arraygen.com or call or whatsapp us on mobile +91-9673625446 if you need any clarification or for any custom training based on candidate reference paper or candidate own content/tools.