Enjoy!🌟
A SNEAK PEEK INTO OUR LAB
Pasilla gene 🧬 encodes a set of proteins that are most similar to those found in humans Nova-1 and Nova-2 are the names of two satellites. Nova-1 and Nova-2 are nuclear RNA-binding proteins that are normally expressed in the CNS and regulate splicing directly.There are numerous applications for RNA sequencing data with a reference genome, and there is no optimal pipeline for all cases. We will go over all the major steps in Reference based RNA-seq data analysis 💻, such as quality control (FastQC, MutiQC, Cutadapt), reads alignment (RNA STAR, IGV), gene and transcript quantification (HT-Seq count), differential gene expression (DEseq2), functional profiling (goseq) and advanced analysis. Using this tutorial, we were able to do differnetial gene expression analysis besides identifying the genes and pathways regulated by the Pasilla gene as they were affected by its depletion. To know more about our adventures 🤯 with the analysis process, don'y hesitate to check the following hyperlinks 🔥🔗. You will explore a lot about the field of transcriptomics in the next minutes 👀
To check out the results of our workflow in galaxy, click on the links below:
Quality_Control | Mapping | Analysis_Visualisation_Functional Enrichment
Click on each image to know the detailed procedure to conduct this analysis step
Getting to the end of our work, are you excited to meet our team members?!! 😍🥳🥳
| Team Sub-groups | Specific Task | Contributors | Slack IDs |
|---|---|---|---|
| Quality Control | Sub-samples | Yasmeen & Eman | @Sam & @Eman |
| Quality Control | Full datasets | Bandana, Jaspreet, Pankaj | @Bandana, @Jaspreet, @Pankaj |
| Quality Control | Markdown Documnetation | Jaspreet, Bandana, Eman | @Eman, @Bandana & @Jaspreet |
| Mapping | Inspection of Mapping Results | Yasmeen, Bandana, Dawoud, Nirvana | @Sam, @Bandana, @Dawoud, @Nirvana |
| Mapping | Counting the number of reads per annotated gene | Yasmeen, Saket, Johny | @Sam, @Saket, @Johny |
| Mapping | Estimation of strandness | Eman, Saket, Johny | @Saket, @Johny, @Eman |
| Mapping | Counting reads per genes | Ankita, Favour, Nirvana | @Anku., @Nirvana, @OYEFAVOUR |
| Mapping | Markdown Documentation | Eman, Yasmeen, Dawoud, Johny | @Sam & @Eman, @Dawoud, @Johny |
| Differential Gene Expression Analysis | Identification of the differentially expressed features | Rana, Utkarsha, Osama, Nikita, Chigozie, Yasmeen, Johny, Shruti | @RanaSalah, @-Utkarsha12-, @Osama, @Nikita2Chimera, @GozieNkwocha, @Sam, @Johny, @ShrutiG |
| Differential Gene Expression Analysis | Extraction of annotation of differentially expressed genes | Utkarsha, Osama, Rana, Jaspreet, Nikita, Chigozie | @RanaSalah, @-Utkarsha12-, @Osama, @Nikita2Chimera, @GozieNkwocha, @Jaspreet |
| Differential Gene Expression Analysis | Markdown Documentation | Rana | @RanaSalah |
| Visualization of the DE genes' expression | Visualization of the normalized counts | Osama, Utkarsha, Rana, Ankita, TosinA, Dawoud | @RanaSalah, @-Utkarsha12-, @Osama, @Anku., @TosinA, @Dawoud |
| Visualization of the DE genes' expression | Computation & Visualization of the Z-score | Saket, Utkarsha, Osama, Rana, Ankita, TosinA, Diyar | @Saket, @RanaSalah, @-Utkarsha12-, @Osama, @Anku., @TosinA, @diyar |
| Visualization of the DE genes' expression | Markdown Documentation | Osama, Jaspreet, Utkarsha | @Osama, @Jaspreet, @-Utkarsha12- |
| Functional enrichment analysis of the DE genes | Gene Ontology analysis | Amira, TosinA, Bandana, Johny, Shruti | @Amira, @TosinA, @Bandana, @Johny, @ShrutiG |
| Functional enrichment analysis of the DE genes | KEGG pathways analysis | Amira, TosinA, Chigozie, Rana | @Amira, @TosinA, @GozieNkwocha, @RanaSalah |
| GitHUb Markdown Development | Format & Organization | Main ReadMe: Utkarsha, Osama, Rana, Ankita, TosinA, Bandana. Quality control: Jaspreet. Mapping: Saket, Yasmeen, Johny, Dawoud. Differential Gene Expression Analysis: Rana. Visualization: Osama, Jaspreet, Utkarsha. Functional Enrichment Analysis: TosinA | @RanaSalah, @-Utkarsha12-, @Osama, @Anku., @TosinA, @Bandana, @Jaspreet, @Sam, @Saket, @Johny, @Dawoud |
| Graphical Abstract Design | Rana, Osama, Jaspreet, Ankita, Diyar | @RanaSalah, @Osama, @Jaspreet, @Anku., @diyar | |
| Advertisement | Writing post on transfer-market | Tosin | @TosinA |
| Training | Moderated the training workshops & presented the workflow steps practically | Quality control: Yasmeen & Jaspreet. Mapping: Saket, Yasmeen. Differential Gene Expression Analysis: Rana & Osama. Visualization: Osama. Functional Enrichment Analysis: Amira | @Sam & @Jaspreet, @Saket, @RanaSalah, @Osama, @Amira |
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Used usegalaxy.org: "The sequencing data were uploaded to the Galaxy web platform, and we used the public server at usegalaxy.org to analyze the data ( Brooks et al. 2011)."
