PPT-RIP – Transcript Expression Levels

Outline RNA ImmunoPrecipitation RIP NGS on RIP amp its alternatives Alternate splicing Transcription as a graph Distribution of tags in exons Pipeline on RIPseq dataset RNA ImmunoPrecipitation RIP. Unveiling . the Transcriptome using . RNA-. seq. Jinze. Liu. Outline. What is the transcriptome?. Measuring the transcriptome. Sampling the transcriptome using short reads. Alignment of reads to a reference genome. Bioinformatics . Workshop:. RNA . Seq. using Galaxy. Typical . RNA_Seq. Project Work Flow. Sequencing. Tissue Sample. . Cufflinks. . TopHat. FASTQ file. . QC. . Gene/Transcript/. Exon. Expression. Alisha Holloway, PhD. Gladstone Bioinformatics Core Director. What is RNA-seq?. Use of high-throughput sequencing technologies to assess the RNA content of a sample.. Why do an RNA-seq experiment?. Detect . from Ion . Torrent RNA-Seq Data. Alex Zelikovsky . Department of Computer Science. Georgia State University. Joint work with Serghei Mangul, . Sahar . Al . Seesi, Adrian . Caciula, Dumitru Brinza. , . . in wounds undergoing negative pressure wound therapy. Nate . Stearrett. (presentation format shamelessly stolen from Jeff . Elhai. ). Chronic Wounds. http://wjes.biomedcentral.com/articles/10.1186/1749-7922-2-10. RNA-. seq. BMI 877. Spring . 2017. Colin Dewey. colin.dewey@wisc.edu. Overview. Some motivation: axolotl. RNA-. seq. . technology. The . RNA-. seq. . quantification problem. Generative probabilistic models and Expectation-Maximization for the quantification task. What is a transcript, . and why is it important?. Your high school transcript is the official school record of your high school classes, grades, and attendance. It also includes your ACT scores, GPA, and Class Rank. . Inselspital. Department for Clinical Research, University of Bern. 1.6.2017. Introduction. Autotaxin. (ATX) . is a secreted . lysophospholipase. D catalyzing hydrolysis of . lysophosphatidylcholine. An Data . Analysis . Activity. . for Students. . This . teacher slide set was . created by Dana Haine, MS, of the UNC . Superfund Research Program, . which is funded by the National Institute of Environmental Health Sciences (P42ES005948. Marina DiStefano, Ph.D.. Clinical Molecular Genetics Fellow, . Harvard Medical School Genetics Training Program. Biocurator Call, 1.10.19. Outline. Why does transcript curation matter? Examples from Hearing Loss. Seq. Sequenced reads. cells. sequencer. cDNA. ChIP. genome. read coverage. Alignment. Once sequenced the problem becomes . computational. Considerations and assumptions. High library complexity. #molecules in library >> #sequenced molecules. Jeremy Buhler. for GEP Alumni Workshop. RNA-Seq Pipeline for Expression Analysis. RNA Source. 37251. 20653. 9827. 5121. RNA-Seq Read Count . per Transcript. Map reads to transcripts. RNA Abundance. Dr. Xiangyu Li. KTH-Royal In. stitute. of Technology. http://sysmedicine.com. 1. Where the transcripts come from?. 2. Pre-mRNA. Intron. Patterns . of alternative . splicing. 3. HPA 37 different human tissues. cART. ) in aged HIV-1-infected individuals could enhance the incidence of clinical manifestations such as chronic kidney disease (CKD). Specifically, . the use of TDF has been associated with increased kidney function deterioration, but recent studies did not find an increased rate of renal disease in patients with low risk for renal involvement or in those receiving non-boosted .