BackgroundNext-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS data analysis remains a challenging, time-consuming, and often irreproducible process. Therefore, there is a need for a comprehensive and flexible workflow platform that can accelerate data processing and analysis so more time can be spent on functional studies.ResultsWe have developed an integrative, stand-alone workflow platform, named CIPHER, for the systematic analysis of several commonly used NGS datasets including ChIP-seq, RNA-seq, MNase-seq, DNase-seq, GRO-seq, and ATAC-seq data. CIPHER implements various open source software packages, in-house scripts, and Docker containers to analyze and process single-ended and pair-ended datasets. CIPHER’s pipelines conduct extensive quality and contamination control checks, as well as comprehensive downstream analysis. A typical CIPHER workflow includes: (1) raw sequence evaluation, (2) read trimming and adapter removal, (3) read mapping and quality filtering, (4) visualization track generation, and (5) extensive quality control assessment. Furthermore, CIPHER conducts downstream analysis such as: narrow and broad peak calling, peak annotation, and motif identification for ChIP-seq, differential gene expression analysis for RNA-seq, nucleosome positioning for MNase-seq, DNase hypersensitive site mapping, site annotation and motif identification for DNase-seq, analysis of nascent transcription from Global-Run On (GRO-seq) data, and characterization of chromatin accessibility from ATAC-seq datasets. In addition, CIPHER contains an “analysis” mode that completes complex bioinformatics tasks such as enhancer discovery and provides functions to integrate various datasets together.ConclusionsUsing public and simulated data, we demonstrate that CIPHER is an efficient and comprehensive workflow platform that can analyze several NGS datasets commonly used in genome biology studies. Additionally, CIPHER’s integrative “analysis” mode allows researchers to elicit important biological information from the combined dataset analysis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1770-1) contains supplementary material, which is available to authorized users.
A series of three annual surveys of David Geffen School of Medicine (DGSOM) at UCLA students and UCR/UCLA Thomas Haider Program in Biomedical Sciences students were administered from 2010 to 2012 to ascertain student perceptions of which anatomy pedagogy-prosection or dissection-was most valuable to them during the first year of preclinical medical education and for the entire medical school experience in general. Students were asked, "What value does gross anatomy education have in preclinical medical education?" We further asked the students who participated in both prosection and dissection pedagogies, "Would you have preferred an anatomy curriculum like the Summer Anatomy Dissection during your first year in medical school instead of prosection?" All students who responded to the survey viewed anatomy as a highly valued part of the medical curriculum, specifically referring to four major themes: Anatomy is (1) the basis for medical understanding, (2) part of the overall medical school experience, (3) a bridge to understanding pathology and physiology, and (4) the foundation for clinical skills. Students who participated in both prosection and dissection pedagogies surprisingly and overwhelmingly advocated for a prosection curriculum for the first year of medical school, not a dissection curriculum. Time efficiency was the dominant theme in survey responses from students who learned anatomy through prosection and then dissection. Students, regardless of whether interested in surgery/radiology or not, appreciated both pedagogies but commented that prosection was sufficient for learning basic anatomy, while dissection was a necessary experience in preparation for the anatomical medical specialties. This suggests that anatomy instruction should be integrated into the clinical years of medical education.
There are categorical structural alterations in the ventricular system of myelomeningocele patients that are well correlated with previous necropsy and imaging reports. The ventricular system of dysraphic children presents severe anatomic alterations, which alter the reference points of the classical endoscopic third ventricular cisternostomy.
The transition of RNA polymerase II (Pol II) from transcription initiation into productive elongation in eukaryotic cells is regulated by the P-TEFb kinase, which phosphorylates the C-terminal domain of paused Pol II at promoter-proximal regions. Our recent study found that P-TEFb (in an inhibited state bound to the 7SK snRNP complex) interacts with the KAP1/TRIM28 transcriptional regulator, and that KAP1 and the 7SK snRNP co-occupy most gene promoters containing paused Pol II. Here we provide a detailed experimental description and analysis of the ChIP-seq datasets that have been deposited into Gene Expression Omnibus (GEO): GS72622, so that independent groups can replicate and expand upon these findings. We propose these datasets would provide valuable information for researchers studying mechanisms of transcriptional regulation including Pol II pausing and pause release.
A large body of work has revealed fundamental principles of HIV-1 integration into the human genome.However, the effect of the integration site to proviral transcription activity has so far remained elusive.Here we combine open-source, large-scale datasets including epigenetics, transcriptome, and 3D genome architecture to interrogate the chromatin states, transcription activity landscape, and nuclear sub-compartments around HIV-1 integration sites in CD4 + T cells to decipher human genome codes shaping the transcription of proviral classes defined based on their position and orientation in the genome. Using a Hidden Markov Model, we describe the importance of specific chromatin states and genome architecture in the control of HIV-1 transcription activity. Additionally, implementation of a machine-learning logistic regression model reveals upstream chromatin accessibility, transcription activity, and categorical nuclear sub-compartments as optimal features predicting HIV-1 transcriptional outcomes. We finally demonstrate clinical relevance by interrogating the positions of intact proviruses persisting in patients under suppressive therapy and provide a compass compatible with clinical decision-making.
In this project, Matlab® computational and visualization tools were used to develop user-friendly software, called 3D Transient Heat Flow. With this interactive software, the students can run a wide variety of the experiments with different materials, boundary conditions and geometry at transient conditions. It is interesting to note that running some of these experiments in traditional labs is impossible. The software presents experimental results in colored graphical diagrams as well as tables and charts, which can be compared easily with the results of previous experiments. In order to evaluate and validate the reliability of the software, a case study is considered, in which the results obtained using the software are compared with those obtained using computational fluid dynamics code, such as the Fluent® package.
We describe student beliefs of how anatomy education influenced their preparation for standardized clinical assessments and clinical skills. We conducted three annual surveys of students of the David Geffen School of Medicine (DGSOM) at the University of California Los Angeles (UCLA) and students of the University of California, Riverside (UCR)/UCLA Thomas Haider Program in Biomedical Sciences from 2010 to 2012. Students were asked, "What specific knowledge or skills did you learn from your gross anatomy experience that helped you prepare for USMLE board exams, third-year clerkships, and physical examination skills?" All students who responded to the survey viewed anatomy as a highly valued part of the medical curriculum. Almost all students felt that anatomy knowledge in general was useful for their success with United States Medical Licensing Examination (USMLE) exams, how they perceived their physical exam skills, and how they perceived their preparation for third-or fourth-year clerkships. On the other hand, when asked about how the anatomy curriculum helped prepare students for fourth-year clerkships, there was a downward trend over a three-year period with each subsequent class. Although anatomy is a highly valued part of the medical school experience, students value integration of the anatomical and clinical sciences, as evidenced by a perceived diminishing value of anatomy pedagogy taught outside of clinical context with subsequent classes over the course of three years.
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