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SPATIAL TRANSCRIPTOMICS

10-Day Certificate Online Training in NGS Data Analysis | Spatial Transcriptomics Analysis

4.7

Resource Person : Event Date :- 1 Nov ,2024 - 31 Dec, 2025. Event Timing :- Any time you choose, either from 6:30 AM-8 AM or 10 PM-11:30 PM India time.

This Courses Included

  • High demand video
  • Learn from Experts
  • Hands-on practical sessions
  • Certificate on completion

BDG LifeSciences is a distinguished bioinformatics company established in 2010 and operates globally. Headquartered in India the company specializes in facilitating workshops, training programs, novel & innovative research projects, and online courses in technologies of bioinformatics & life science. The company is registered under the Ministry of MSME (Micro, Small, and Medium Enterprises), Government of India, with the registration number UDYAM-UP-01-0019151. Recently, BDG Lifesciences, India has authorized BBR Group Pty Ltd., Australia (ACN 608 550 849), to operate its programs in Australia & New Zealand.
With a focus on practical application of technology, where participants work on their own computer/laptop on software/servers,  BDG LifeSciences has been a leader in the sector for the last 14 years. Since its inception, BDG LifeSciences has successfully educated a diverse range of participants globally, including students, scientists, faculty members, professors, and corporate executives.

 

We have launched our 10-day Online Technical Training in Next Generation Sequencing | Spatial Transcriptomics Analysis on Windows, Linux & Mac OS. It will be an extensive 10-day training program in which every day 60 minutes interactive training sessions will be conducted to give the user a unique learning experience. VIDEO RECORDING WILL BE PROVIDED. On successful completion of the course participation certificate will be awarded.

As it is 100% hands-on training program participants will run the processes on their own computer systems having Windows/ Mac/ Linux with a unique learning experience. The program will be of great help to students/ researchers/ faculty/ pathologists/ scientists in learning this latest technology.

 

WHY THIS COURSE IS IMPORTANT?

Spatial transcriptomics has become essential for biomedical research, particularly in developmental biology, cancer, immunology, and neuroscience. To understand normal development and disease pathology, it is crucial to understand the relationship between cells and their relative locations within tissues. With the use of spatial transcriptomics, a cutting-edge technique in molecular profiling, researchers may map the locations of all the genes active in a tissue sample and assess each gene's activity. The position of any given cell, relative to its neighbours and non-cellular structures, can provide helpful information for defining cellular phenotype, cell state, and ultimately cell and tissue function. Location can determine the signals to which cells are exposed. Spatial transcriptomics techniques use intact tissue sections, spatial barcoding, or in situ hybridization to retain positional information. Scientists are already using this technology to assist them in comprehending biological processes and diseases since it is yielding fresh findings..

Research Highlights using Spatial Transcriptomics Analysis

  • Immunological Atlas
  • Understanding the Tumor Microenvironment
  • Examine gene expression in the context of the tissue microenvironment
  • Spatially Mapping Diverse Tissues

SCHEDULE

DAY

MODULE

TOPICS

1

Module 1: Introduction to NGS

  • NGS overview
    • Evolution of sequencing:1st, 2nd & 3rd generation sequencing
    • High throughput sequencing workflow

2

Module 2: Genomics file format

  • FASTA,FASTQ,BAM/SAM/CRAM

3

Module 3: Introduction to spatial  transcriptomics

  • RNA-seq technology overview
  • Single-cell RNA technology overview
  • Spatial transcriptomics overview

4

Module 4: Linux command line and shell scripting

  • Basic Linux command line
  • Shell scripting basics

5

Module 5:10X Visium  technology

  • Visium technology
  • 10X data exploration
    • Processing raw 10X Genomics spatial  transcriptomics data
    • Explore the output of Space Ranger

6

Module 6: Seurat Object

  • Seurat package
  • Installing required packages
  • Exploring raw data (count matrix file)
  • Creating Seurat object
  • Exploring Seurat object structure

7

Module 7:Quality control

  • Quality control
  • Generation quality control plots

8

Module 8: Integration methods

  • Batch effect correction
  • Different batch effect correction methods

9

Module 9: Downstream process

  • Introduction to Normalization
  • Log Normalization, SC Transform
  • PCA

10

Module 10: Clustering and finding marker genes and cell annotation

  • Clustering
  • Generating UMAP/t-SNE plots
  • Finding cluster biomarkers
  • Marker gene expression profile
  • Generate violin and feature plot
  • Cell annotation

SYSTEM REQUIREMENT: Any OS (Windows/Mac/Ubuntu) with internet connection

PRE-REQUISITES: 

  • Mobaxterm if using windows operating system
  • Basic knowledge of R.

LEARNING OUTCOMES: What will I learn? After this course, you should be able to:

  1. Understanding of NGS and spatial transcriptomics
  2. Describe the range of sequencing technologies available, their pros and cons, and which you may want to use for your experiments.
  3. Understanding of biological data and how to extract information from it
  4. Explain the steps in the spatial transcriptomics pipeline
  5. Compute and assess QC metrics at every step in the workflow
  6. Cluster cells based on expression data and derive the identity of the different cell types present
  7. Perform integration of different sample conditions. 
  8. Apply differential expression and cell abundance between conditions
  9. Repeat the course analysis of spatial transcriptomics on your data to do end-to-end analysis
  10. Recognize decision-making steps along the analysis pipeline and justify your decisions, from data exploration to final visualization.

TARGET AUDIENCE

Student: Bachelor, Masters, PhD, MBBS, MD students as well as Faculty and Professors from Microbiology, Biochemistry, Biotechnology, Immunology, Medicine, Pharmacy, Pharmaceutical Chemistry, Biomedical Technology, Genetics, Bioinformatics, Plant Science and Life Sciences.

Professionals: Resident Doctors, Biotechnology, Bioinformatics, Medicine and Pharmaceutical scientists from industry, academia, and regulatory agencies. Hands-on exercises will be performed individually using software tools on your own laptops. (no prior experience required).

 

RESOURCE PERSON

Ashish Kumar Choudhary, a Technical Associate at BDG Lifesciences and a graduate of the Indian Institute of Technology (IIT) Bombay, specializes in bioinformatics, sequencing data analysis, and computational biology. With expertise in scRNA-Seq, spatial transcriptomics, RNA-Seq, and DNA-Seq, Ashish excels in building optimized pipelines and solving complex problems using R, Python, and C programming. His academic and professional experiences, including hands-on research at the National Centre for Microbial Resource in Pune, reflect his strong foundation in genomics, next-generation sequencing, and metagenomics. Dedicated to leveraging genomics data for biomedical advancements, Ashish conducts impactful workshops, training sessions, and research projects aimed at addressing challenges in precision medicine.

 

REGISTRATION STEPS:

  1. Click on register tab.
  2. This will take you to this link- https://events.humanitix.com/bdg-lifesciences-training-programs/tickets
  3. You will see the Training Programs and their fee, scroll down to see the list of all available training programs.
  4. For the training which you want to register, click 1 for 1 participant, 2 for 2 participants and so on and then click Continue.
  5. Fill in the required attendee information and proceed to payment.
  6. Complete the payment process, and you will receive your registration/ticket via email.

T & C

  • After registering, please email to info@bdglifesciences.com with your preferred start date and choose one of the following time slots: 6:30 AM–8:00 AM India time or 9:30 PM–11:00 PM India time.
  • Kindly note that the time of the sessions will be 60-90 minutes everyday. 
  • Once you register, please allow us 2-5 working days to make your training schedule,i.e. dates and time.
  • Please provide a GMAIL ID for registration as the recorded video session will be provided on YouTube. Kindly provide that email ID by which you use YouTube.
  • Since the training is a one-on-one live session with a trainer on Zoom, you'll need to attend, allowing for practical hands-on learning, real-time explanations, and direct query resolution for a better learning experience.
  • At the end of each session, you will receive a video recording, allowing you to review the steps as many times as needed to enhance your learning and master the topics and tasks.
  • BDG Lifesceiences (OPC) Private Limited is registered under Ministry of MSME(Micro, Small and Medium Enterprises), Government of India with Registration Number:UDYAM-UP-01-0019151 hence the certificate will be provided of it. BBR Group Pty Ltd, Australia (ACN-Australian Company Number-608 550 849) has the franchisee of BDG Lifesciences to run its programs in Australia & New Zealand.
  • The certificate will be issued as per the details which you will provide in the registration form while registering before payment.
  • We want to make sure that you learn properly hence the training certificate will be given ONLY on successful completion of all the tasks given by the trainer.
  • The certificates of all our Online programs are sent by email(softcopy) which has a unique barcode. You can take a print of that on heavy cardstock or photo paper and get it laminated if required.
  • The registration is NON-REFUNDABLE and NON-TRANSFERABLE.
  • BDG Lifesciences (OPC) Pvt. Ltd., India and BBR Group Pty Ltd Australia reserves the right of admission in all our programs.
  • If you are removed or your registration is canceled then there will be no answer to that. We have our own reasons for such an act of ours. If we do not wish to give this workshop to any participant then we will refund their amount.
  • To view the pictures of our previous events click here-1 and click here-2. To view, the listing of upcoming events kindly click here and our previous workshops can be viewed here. To view the video feedback of our previous events kindly visit our YouTube Channel
  • You should also read the Terms & Conditions page as well as the FAQs page. For any assistance kindly chat with our AI Assistant BioBot on the website www.bdglifesciences.com
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