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hepatocellular_carcinoma [2020/12/07 22:25] – [Data] adminhepatocellular_carcinoma [2020/12/07 22:27] – [Related software] admin
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   - [[http://gqinnovationcenter.com/documents/bioinformatics/RNAseq_Cuba_OMICS_2013.pdf|Lefebvre's]] quick tutorial on RNA-Seq data analysis.   - [[http://gqinnovationcenter.com/documents/bioinformatics/RNAseq_Cuba_OMICS_2013.pdf|Lefebvre's]] quick tutorial on RNA-Seq data analysis.
   - Schiffthaler's ~1 hour video on RNA Seq data [[https://www.youtube.com/watch?v=1rNEkWSxB5s|preprocessing]] including FastQC, sortmerna to exclude rRNA, trimmomatic to trim the adaptors and low quality bps, STAR to map reads to the genome, samtools to index the bam file, IGV to visualize the reads on the genome, and HTSeq to count the number of reads mapped to each gene (coverage). These are all steps we need to do before differential analysis using, say DESeq2. [[http://www.epigenesys.eu/images/stories/protocols/pdf/20150303161357_p67.pdf|This]] is a textual version explaining the same steps.   - Schiffthaler's ~1 hour video on RNA Seq data [[https://www.youtube.com/watch?v=1rNEkWSxB5s|preprocessing]] including FastQC, sortmerna to exclude rRNA, trimmomatic to trim the adaptors and low quality bps, STAR to map reads to the genome, samtools to index the bam file, IGV to visualize the reads on the genome, and HTSeq to count the number of reads mapped to each gene (coverage). These are all steps we need to do before differential analysis using, say DESeq2. [[http://www.epigenesys.eu/images/stories/protocols/pdf/20150303161357_p67.pdf|This]] is a textual version explaining the same steps.
-  - **Protemoe:**  Data-independent analysis Mass spectrometry (DIA-MS) done on 3 HCC cell lines and an immortalized hepatocyte line, each with 3 biological replicates. Our goal is to understand if the APE1 interactome is 1) different in HCC cell lines vs non tumor cells, 2) different between HCC cell lines with overexpressed APEX1 (SNU398 vs Huh7), 3) and how it compares to that described in [[https://www.nature.com/articles/s41598-019-56981-z|Ayyildiz 2020]].+
 [[:hepatocellular_carcinoma|Drafts]], [[:hepatocellular_carcinoma|Next steps]] [[:hepatocellular_carcinoma|Drafts]], [[:hepatocellular_carcinoma|Next steps]]