Group Projects: Chromosome-specific TDP-43 Knockout Analysis

Project Goal

Each group will analyze the effect of TDP-43 knockout on gene expression in their assigned chromosome. Using the same experimental dataset (GSE136366) from the labs, you will apply the complete RNA-seq analysis pipeline to discover chromosome-specific impacts of TDP-43 loss.

Project Overview

Background

TDP-43 is a ubiquitously expressed RNA-binding protein that regulates thousands of target genes across the genome. While the labs focused on chromosome 11, TDP-43's effects are distributed across all chromosomes. Your challenge is to identify:

Which genes on your chromosome are affected by TDP-43 knockout
What biological processes are disrupted
Whether your chromosome has unique or particularly strong responses to TDP-43 loss
Potential links to ALS/FTD pathology based on affected genes

Group Assignments

Each group is assigned one chromosome to analyze. Download your chromosome-specific data using the links below. The download links will be activated later.

Important: Your data contains reads mapped only to your assigned chromosome. Follow the same pipeline from the labs, but use your chromosome-specific reference files.

Group	Members	Data Download
Group - chr1	Zahra Habib Almahal Sarah Mohammed Albogami Zahra Osama Almasre Khalood Mostafa Kamal Mohammedmiah	Download chr1 data
Group - chr2	Itab Mohammed Q Alotaibi Eshragha Gafer Abdalla Mohamed Thikra Mohammed Almuqbil Futun Mohammed Alqahtani	Download chr2 data
Group - chr3	Razan Jamaan Alamri Sumayyah Yousef Alraddadi Suzan Mohammad Mahmoud Miqdad Raghad Saleh Abdullah Alyousef	Download chr3 data
Group - chr4	Sna Ghsan Alfywmee Layan Majed Alharbi Hanyn Abdulaziz Alturki Faten Mazyad Fahad Alroways	Download chr4 data
Group - chr5	Wesam Ahmad Bahitham Mayar Mousa Alzahrani Yara Ahmed Ali Alghamdi Omaimah Ali Hassan Algiraigri	Download chr5 data
Group - chr6	Lama Mabruk Alkhuzaee Bdor Khalid Saud Alharbi Tala Akram Jad Raghad Ahmed Abubaker Alkhateeb	Download chr6 data
Group - chr7	Basmah Mahmoud Alfares Ghadeer Ghazi Alsuliman Shaden Ahmed Y Al Ayidh Sarah Khalid Radi Alfardan	Download chr7 data
Group - chr8	Hebah Ahmed Ali Altheyab Dalia Hamad Saad Al Masud Amal Omar Alhussain Almandeeli Lames Saleh Baraji Mayada Mohammed Elfadil Mohammed	Download chr8 data
Group - chr9	Fatimah Ali Mohammed Hojirat Jody Mohammed Maher Shikh Albasatne Shahad Hassan Sultan Bassfr Yaqeen Hussain H Al Obaidan	Download chr9 data
Group - chr10	Lujain Ahmed Alharbi Mada Zaid Ali Hazazi Fatemah Wasel H Al Haddaf Zainab Malik Alrawaih	Download chr10 data
chr11 is used in the labs - not assigned
Group - chr12	Rola Ahmed Ali Al Tammam Abeer Fahad Abdullah Albakran Lena Khaled Abdullah Alghamdi Asrab Ahmad Banjar	Download chr12 data
Group - chr13	Mona Marwan Yassine Sheikah Adel Bakheet Alotaibi Lama Khalid Mohammed Abu Ajmah Fadia Mohammed M Ashmawi	Download chr13 data
Group - chr14	Reema Saad M Alqahtani Rahmah Maki Abufoor Rana Bokhait Almaari Renad Khalid Saleh Bugis	Download chr14 data
Group - chr15	Rawan Ahmed S Baqar Sara Mohammad T Althaqafi Rana Ali Rashed Alhazzani Lamar Abdullah Abdulaziz Muneer	Download chr15 data
Group - chr16	Thouraya Tayseer AlamEddine Ruba Fawaz Alsulami Raghad Fahad Alotaibi Nagham Hesham Jameel Mojaleed	Download chr16 data
Group - chr17	Eshraq Yahya Hasan Zakri Ruya Shnar Alshakarah Ghaida Tariq Mahmoud Mohammed Remass Mohammed Mosad Ashmawi	Download chr17 data
Group - chr18	Juwairiyah Tameer Islam Zahra Abdulqader M Alakhdhar Hiba Abdeljebbar Elaaiouar Lujain Mohammed Alansari	Download chr18 data
Group - chr19	Yasir Fahad Alnakhli Hussain Faisal Zaid Alharbi Muhammad Shoaib Ashraf Muhammad Mohammed Hanafi Alkhayyat	Download chr19 data
Group - chr20	Ammar Yasir Babasit Abdullah Eyad Abdullah Almokhtar Akeel S Aljarodi Ahmad Abdullah Ali Bukhamsin	Download chr20 data
Group - chr21	Abdullah Waleed Abdullah Misar Raiyan Tarek Mahmoud Subedar Abdulrahman Mohammed Amin Alahmed Turky AbdulHakim Mohammed AlSulaiman	Download chr21 data
Group - chr22	Omar Abdulwahed Buqes Ahmed Abdulrahman Wasel Albishri Syed Umer Hannan Ahmed Abdullah Mubarak Abdullah Alsubaie	Download chr22 data
Group - chrX	Ibrahim Eisi Ibrahim Abu Alghayth Ahmed Hani Mawlawi Haitham Abdulaziz Alahmdi	Download chrX data

Download Contents

Each download includes:

raw_data/ - FASTQ files (6 samples × 2 paired-end files)

Tips for Success

Start Early & Team Work

The computational pipeline takes time. Start your analysis as soon as possible so you have time to interpret results and prepare your presentation.

Compare with Literature

Search PubMed for your top DE genes + "TDP-43" to see if they've been reported before. This adds credibility and context to your findings.

Common Pitfalls to Avoid

Not checking mapping rates (low rates indicate problems)
Forgetting to use the correct chromosome-specific reference files
Over-interpreting results from a small number of DE genes

TDP-43 Background Reading

Original dataset paper: Roczniak-Ferguson & Ferguson, 2019