From 9dde9e489782aad4bc3497dce18ab788b31205af Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 4 Feb 2025 15:28:26 +0000 Subject: [PATCH] Render course --- docs/404.html | 4 ++-- docs/About.md | 10 +++++----- docs/about-the-authors.html | 14 +++++++------- docs/epigenetics-in-the-media.html | 4 ++-- docs/explore-the-epigenome.html | 4 ++-- docs/index.html | 6 +++--- docs/index.md | 3 +-- docs/nature-versus-nurture.html | 4 ++-- docs/search_index.json | 2 +- 9 files changed, 25 insertions(+), 26 deletions(-) diff --git a/docs/404.html b/docs/404.html index a9a6ad9..5005aea 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,7 @@ Page not found | Epigenetics on AnVIL: Nature vs Nurture - + @@ -22,7 +22,7 @@ - + diff --git a/docs/About.md b/docs/About.md index e9d61b8..1b10288 100644 --- a/docs/About.md +++ b/docs/About.md @@ -37,12 +37,12 @@ These credits are based on our [course contributors table guidelines](https://gi ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC -## date 2024-08-06 +## date 2025-02-04 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source -## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1) +## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) @@ -58,7 +58,7 @@ These credits are based on our [course contributors table guidelines](https://gi ## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) ## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) ## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) -## knitr 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34) +## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2) ## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) ## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) ## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) @@ -74,7 +74,7 @@ These credits are based on our [course contributors table guidelines](https://gi ## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) ## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) ## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) -## rmarkdown 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9) +## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0) ## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0) ## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) ## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) @@ -83,7 +83,7 @@ These credits are based on our [course contributors table guidelines](https://gi ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) -## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc) +## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## diff --git a/docs/about-the-authors.html b/docs/about-the-authors.html index 1b3fbed..e027acd 100644 --- a/docs/about-the-authors.html +++ b/docs/about-the-authors.html @@ -6,7 +6,7 @@ About the Authors | Epigenetics on AnVIL: Nature vs Nurture - + @@ -22,7 +22,7 @@ - + @@ -232,12 +232,12 @@

About the Authors Chapter 2 Epigenetics in the Media | Epigenetics on AnVIL: Nature vs Nurture - + @@ -22,7 +22,7 @@ - + diff --git a/docs/explore-the-epigenome.html b/docs/explore-the-epigenome.html index 4f20674..44419e0 100644 --- a/docs/explore-the-epigenome.html +++ b/docs/explore-the-epigenome.html @@ -6,7 +6,7 @@ Chapter 3 Explore the Epigenome | Epigenetics on AnVIL: Nature vs Nurture - + @@ -22,7 +22,7 @@ - + diff --git a/docs/index.html b/docs/index.html index 0c641b5..c7b074a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,7 +6,7 @@ Epigenetics on AnVIL: Nature vs Nurture - + @@ -22,7 +22,7 @@ - + @@ -152,7 +152,7 @@

Overview

diff --git a/docs/index.md b/docs/index.md index 1ed3498..3c85075 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,6 +1,6 @@ --- title: "Epigenetics on AnVIL: Nature vs Nurture" -date: "August 06, 2024" +date: "February 04, 2025" site: bookdown::bookdown_site documentclass: book bibliography: book.bib @@ -41,4 +41,3 @@ Learning objectives for this activity come from the [Genetics Core Competencies] Additional guides are provided to help you with Workspaces, launch interactive tools, and start working with data. Learn more about AnVIL by visiting https://anvilproject.org or reading the [article in Cell Genomics](https://www.sciencedirect.com/science/article/pii/S2666979X21001063). Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/ - diff --git a/docs/nature-versus-nurture.html b/docs/nature-versus-nurture.html index 0bf3ce5..9dc3c7d 100644 --- a/docs/nature-versus-nurture.html +++ b/docs/nature-versus-nurture.html @@ -6,7 +6,7 @@ Chapter 1 Nature versus Nurture | Epigenetics on AnVIL: Nature vs Nurture - + @@ -22,7 +22,7 @@ - + diff --git a/docs/search_index.json b/docs/search_index.json index 25a55c9..78d3b01 100644 --- a/docs/search_index.json +++ b/docs/search_index.json @@ -1 +1 @@ -[["index.html", "Epigenetics on AnVIL: Nature vs Nurture Overview Skills Level Learning Objectives", " Epigenetics on AnVIL: Nature vs Nurture August 06, 2024 Overview This activity is intended to serve as an introduction to the field of epigenetics, or the idea of “nature versus nurture”. The first activity, Explore the Epigenome leverages the UCSC Genome Browser - a powerful tool for visualizing genomic differences. This book is part of a series of books for the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) of the National Human Genome Research Institute (NHGRI). Skills Level Genetics Beginner: minimal prior knowledge/skill helpful Programming skills Novice: no programming experience needed Learning Objectives Learning objectives for this activity come from the Genetics Core Competencies: Discuss how DNA is packaged in the chromosomes in terms of histones, nucleosomes, and chromatin. Defend how most cells can have the same genetic content and yet have different functions in the body. Contrast the packaging of DNA into euchromatin versus heterochromatin in the context of histone modification, and DNA modification (where applicable). Discuss the potential roles of DNA modification, histone modification, and non-coding RNA in epigenetic inheritance, both somatic and germline. Discuss environmental impacts on epigenetic systems. Describe how differential histone modification modulates gene activity and is utilized in developmental progression. AnVIL Collection Additional guides are provided to help you with Workspaces, launch interactive tools, and start working with data. Learn more about AnVIL by visiting https://anvilproject.org or reading the article in Cell Genomics. Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/ "],["nature-versus-nurture.html", "Chapter 1 Nature versus Nurture", " Chapter 1 Nature versus Nurture This lecture module introduces epigenetics. It provides background on DNA packaging within cells, and a review of how epigenetics fits within the “Central Dogma” of molecular biology - the process of turning DNA into RNA into protein. Learning Objectives Answer “what is epigenetics?” Learn to think of epigenetics as “Nature versus Nurture”. You can view and download the Google Slides here. "],["epigenetics-in-the-media.html", "Chapter 2 Epigenetics in the Media 2.1 The Legacy of Trauma: Can Experiences Leave A Biological Imprint? 2.2 Finding out if more than your DNA passes on to the next generation 2.3 Instructions for Life: How Food, Stress, and Our Genes Shape Our Health 2.4 Exploring the history of epigenetics, and what the future may hold for the field 2.5 The Effect of lncRNAs on Chromatin and Gene Regulation (John Rinn)", " Chapter 2 Epigenetics in the Media 2.1 The Legacy of Trauma: Can Experiences Leave A Biological Imprint? Can epigenetics explain why descendants of trauma victims seem to have worse health outcomes? Bianca Jones Marlin and Brian Dias dive into epigenetics and its role in trauma inheritance on the Shortwave Podcast. 2.2 Finding out if more than your DNA passes on to the next generation In this episode of Genetics Unzipped, Dr. Kat Arney takes a look at the world of epigenetics - finding out if more than DNA passes on to the next generation, whether Darwin was wrong and Lamarck was right, and how to pimp your genome. 2.3 Instructions for Life: How Food, Stress, and Our Genes Shape Our Health In this episode of Population Healthy, Experts from the University of Michigan School of Public Health unpack how our genes respond to changes in our diets, stress levels, and exposure to toxins—and what these interactions mean for human health. 2.4 Exploring the history of epigenetics, and what the future may hold for the field In this Nature Podcast Extra, Nick Howe speaks to Edith Heard, Director General of the EMBL, and Giacomo Cavalli, from the Institute of Human Genetics, exploring the history and future of epigenetics. 2.5 The Effect of lncRNAs on Chromatin and Gene Regulation (John Rinn) In this episode of Epigenetics Podcast, Dr. John Rinn from the University of Colorado in Boulder discusses the role of long noncoding RNAs (lncRNAs) in regulating the expression of genes and chromatin organization. "],["explore-the-epigenome.html", "Chapter 3 Explore the Epigenome 3.1 Launch the Genome Browser Gateway 3.2 Clean up Visual Settings 3.3 Zooming Out 3.4 Selecting Histone Marks 3.5 Comparing Histone Marks", " Chapter 3 Explore the Epigenome 3.1 Launch the Genome Browser Gateway Go to https://genome.ucsc.edu/cgi-bin/hgGateway. Ensure “Human” is selected under “Browse/Select Species”. You will be working from the Human Assembly March 2006 (NCBI/hg18). Make sure this is selected under the “Find Position” dropdown menu. Enter HOXA7 in Position/Search Term and select GO. Your Genome Browser should now look like this: 3.2 Clean up Visual Settings You’ll now use the following directions to remove the default visual settings. Scroll below to different menu options shown. Under the “Mapping and Sequence” tab, Base Position should be set to dense. Under the “Genes and Gene Predictions” tab, RefSeq Genes should be set to pack. All other features should be marked as hide. You will need to go through each of the menu options to make sure features are marked as “hide”. Please note you will need to open each menu option by select the “+” to ensure all tracks are turned off (marked as hide). At the end of the browser page, select “refresh”. Your browser should look like the image below, where only HOXA7 is shown. 3.3 Zooming Out Zoom out your display by 10x, 3x or 1.5x to see HOXA1-HOXA13 genes on your browser. The zoom out value you’ll select will be dependent on your computer display screen. You may need to use the zoom in option if you’ve zoomed out the display beyond the HOXA1-HOXA13 genes. Zoom buttons can be clicked more than once. Ideally your browser should like the image below. Instead of zooming in and out, you can always manually enter your chromosome region of choice. For this exercise, try entering the following region: chr7:27,087,367-27,235,317. Click “go”. You could also enter chr7:27,087,367-27,235,317 in the search bar at the start of this exercise instead of HOXA7. 3.4 Selecting Histone Marks Now we’ll visualize histone marks to show that the same chromosome locus can have drastically different histone patterns. Scroll down to the “Regulation” menu and click the Broad Histone track hyperlink. Scroll down and deselect all boxes. Select H3K4me3 and H3K27me3 marks for H1-hESC and NHLF. To learn more about these options you can click on their blue hyperlinks for more information. H3K4me3 is a known histone mark on Histone 3 (H3). It occurs on lysine 4 (K4) and has three methyl groups (me3) that indicate active gene expression. In other words, the DNA is open and ready to be accessed. H3K27me3 is a known histone mark on on Histone 3 (H3). It occurs on lysine 27 (K27) and has three methyl groups (me3) that indicate inactive gene expression. In other words, the DNA is closed off and cannot be accessed. The H1-hESC cell line consists of embryonic stem cells. The NHLF cell line consists of lung fibroblasts. Fibroblasts are important for building the connective structures around cells and healing wounds. Scroll below and deselect the Peak views. You will only need Signal views. Your selected subtracks should only display Signal views as shown below. Click “Submit”. Scroll down, and your browser should look like the image below. 3.5 Comparing Histone Marks Let’s first examine the H1-hESC cell line (embryonic stem cells). Signals are high for the H3K27me3 histone mark. You’ll also notice that H3K4me3 signals are minimal. This signal pattern demonstrates that embryonic stem cells are in the repressed chromatin configuration at the HOXA locus and indicates that HOXA genes in blue are not expressed in this cell line. Now, let’s examine the NHLF cell line (lung fibroblasts). The pattern is different for NHLF. H3K4me3 signals are high for the first half of the HOXA locus, but low for the second half of the locus. H3K27me3 signals are low and then high for the same locus. This signal pattern demonstrates that for lung fibroblasts only half of the HOXA locus is expressed while the other half is not expressed. Specifically, we can use the full image to see that HOXA1-7 are expressed (turned on). We can also see that HOXA9-13 is not expressed (turned off). "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on our course contributors table guidelines.     Credits Names Pedagogy Lead Content Instructor Ifeoma Nwigwe Content Reviewers Elizabeth Humphries, Natalie Kucher Content Director Ava Hoffman Technical Course Publishing Engineer Ava Hoffman Template Publishing Engineers Candace Savonen, Carrie Wright Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Candace Savonen Package Developers (ottrpal) John Muschelli, Candace Savonen, Carrie Wright Funding Funder [National Human Genome Research Institute (NHGRI)] #5U24HG010263 Funding Staff Fallon Bachman, Jennifer Vessio, Emily Voeglein   ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.3.2 (2023-10-31) ## os Ubuntu 22.04.4 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-08-06 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) ## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) ## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) ## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) ## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) ## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) ## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) ## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) ## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) ## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) ## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) ## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) ## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) ## knitr 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34) ## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) ## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) ## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) ## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) ## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) ## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) ## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) ## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) ## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) ## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) ## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) ## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) ## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) ## rmarkdown 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9) ## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0) ## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) ## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) ## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) ## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) ## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library ## ## ────────────────────────────────────────────────────────────────────────────── "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]] +[["index.html", "Epigenetics on AnVIL: Nature vs Nurture Overview Skills Level Learning Objectives", " Epigenetics on AnVIL: Nature vs Nurture February 04, 2025 Overview This activity is intended to serve as an introduction to the field of epigenetics, or the idea of “nature versus nurture”. The first activity, Explore the Epigenome leverages the UCSC Genome Browser - a powerful tool for visualizing genomic differences. This book is part of a series of books for the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) of the National Human Genome Research Institute (NHGRI). Skills Level Genetics Beginner: minimal prior knowledge/skill helpful Programming skills Novice: no programming experience needed Learning Objectives Learning objectives for this activity come from the Genetics Core Competencies: Discuss how DNA is packaged in the chromosomes in terms of histones, nucleosomes, and chromatin. Defend how most cells can have the same genetic content and yet have different functions in the body. Contrast the packaging of DNA into euchromatin versus heterochromatin in the context of histone modification, and DNA modification (where applicable). Discuss the potential roles of DNA modification, histone modification, and non-coding RNA in epigenetic inheritance, both somatic and germline. Discuss environmental impacts on epigenetic systems. Describe how differential histone modification modulates gene activity and is utilized in developmental progression. AnVIL Collection Additional guides are provided to help you with Workspaces, launch interactive tools, and start working with data. Learn more about AnVIL by visiting https://anvilproject.org or reading the article in Cell Genomics. Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/ "],["nature-versus-nurture.html", "Chapter 1 Nature versus Nurture", " Chapter 1 Nature versus Nurture This lecture module introduces epigenetics. It provides background on DNA packaging within cells, and a review of how epigenetics fits within the “Central Dogma” of molecular biology - the process of turning DNA into RNA into protein. Learning Objectives Answer “what is epigenetics?” Learn to think of epigenetics as “Nature versus Nurture”. You can view and download the Google Slides here. "],["epigenetics-in-the-media.html", "Chapter 2 Epigenetics in the Media 2.1 The Legacy of Trauma: Can Experiences Leave A Biological Imprint? 2.2 Finding out if more than your DNA passes on to the next generation 2.3 Instructions for Life: How Food, Stress, and Our Genes Shape Our Health 2.4 Exploring the history of epigenetics, and what the future may hold for the field 2.5 The Effect of lncRNAs on Chromatin and Gene Regulation (John Rinn)", " Chapter 2 Epigenetics in the Media 2.1 The Legacy of Trauma: Can Experiences Leave A Biological Imprint? Can epigenetics explain why descendants of trauma victims seem to have worse health outcomes? Bianca Jones Marlin and Brian Dias dive into epigenetics and its role in trauma inheritance on the Shortwave Podcast. 2.2 Finding out if more than your DNA passes on to the next generation In this episode of Genetics Unzipped, Dr. Kat Arney takes a look at the world of epigenetics - finding out if more than DNA passes on to the next generation, whether Darwin was wrong and Lamarck was right, and how to pimp your genome. 2.3 Instructions for Life: How Food, Stress, and Our Genes Shape Our Health In this episode of Population Healthy, Experts from the University of Michigan School of Public Health unpack how our genes respond to changes in our diets, stress levels, and exposure to toxins—and what these interactions mean for human health. 2.4 Exploring the history of epigenetics, and what the future may hold for the field In this Nature Podcast Extra, Nick Howe speaks to Edith Heard, Director General of the EMBL, and Giacomo Cavalli, from the Institute of Human Genetics, exploring the history and future of epigenetics. 2.5 The Effect of lncRNAs on Chromatin and Gene Regulation (John Rinn) In this episode of Epigenetics Podcast, Dr. John Rinn from the University of Colorado in Boulder discusses the role of long noncoding RNAs (lncRNAs) in regulating the expression of genes and chromatin organization. "],["explore-the-epigenome.html", "Chapter 3 Explore the Epigenome 3.1 Launch the Genome Browser Gateway 3.2 Clean up Visual Settings 3.3 Zooming Out 3.4 Selecting Histone Marks 3.5 Comparing Histone Marks", " Chapter 3 Explore the Epigenome 3.1 Launch the Genome Browser Gateway Go to https://genome.ucsc.edu/cgi-bin/hgGateway. Ensure “Human” is selected under “Browse/Select Species”. You will be working from the Human Assembly March 2006 (NCBI/hg18). Make sure this is selected under the “Find Position” dropdown menu. Enter HOXA7 in Position/Search Term and select GO. Your Genome Browser should now look like this: 3.2 Clean up Visual Settings You’ll now use the following directions to remove the default visual settings. Scroll below to different menu options shown. Under the “Mapping and Sequence” tab, Base Position should be set to dense. Under the “Genes and Gene Predictions” tab, RefSeq Genes should be set to pack. All other features should be marked as hide. You will need to go through each of the menu options to make sure features are marked as “hide”. Please note you will need to open each menu option by select the “+” to ensure all tracks are turned off (marked as hide). At the end of the browser page, select “refresh”. Your browser should look like the image below, where only HOXA7 is shown. 3.3 Zooming Out Zoom out your display by 10x, 3x or 1.5x to see HOXA1-HOXA13 genes on your browser. The zoom out value you’ll select will be dependent on your computer display screen. You may need to use the zoom in option if you’ve zoomed out the display beyond the HOXA1-HOXA13 genes. Zoom buttons can be clicked more than once. Ideally your browser should like the image below. Instead of zooming in and out, you can always manually enter your chromosome region of choice. For this exercise, try entering the following region: chr7:27,087,367-27,235,317. Click “go”. You could also enter chr7:27,087,367-27,235,317 in the search bar at the start of this exercise instead of HOXA7. 3.4 Selecting Histone Marks Now we’ll visualize histone marks to show that the same chromosome locus can have drastically different histone patterns. Scroll down to the “Regulation” menu and click the Broad Histone track hyperlink. Scroll down and deselect all boxes. Select H3K4me3 and H3K27me3 marks for H1-hESC and NHLF. To learn more about these options you can click on their blue hyperlinks for more information. H3K4me3 is a known histone mark on Histone 3 (H3). It occurs on lysine 4 (K4) and has three methyl groups (me3) that indicate active gene expression. In other words, the DNA is open and ready to be accessed. H3K27me3 is a known histone mark on on Histone 3 (H3). It occurs on lysine 27 (K27) and has three methyl groups (me3) that indicate inactive gene expression. In other words, the DNA is closed off and cannot be accessed. The H1-hESC cell line consists of embryonic stem cells. The NHLF cell line consists of lung fibroblasts. Fibroblasts are important for building the connective structures around cells and healing wounds. Scroll below and deselect the Peak views. You will only need Signal views. Your selected subtracks should only display Signal views as shown below. Click “Submit”. Scroll down, and your browser should look like the image below. 3.5 Comparing Histone Marks Let’s first examine the H1-hESC cell line (embryonic stem cells). Signals are high for the H3K27me3 histone mark. You’ll also notice that H3K4me3 signals are minimal. This signal pattern demonstrates that embryonic stem cells are in the repressed chromatin configuration at the HOXA locus and indicates that HOXA genes in blue are not expressed in this cell line. Now, let’s examine the NHLF cell line (lung fibroblasts). The pattern is different for NHLF. H3K4me3 signals are high for the first half of the HOXA locus, but low for the second half of the locus. H3K27me3 signals are low and then high for the same locus. This signal pattern demonstrates that for lung fibroblasts only half of the HOXA locus is expressed while the other half is not expressed. Specifically, we can use the full image to see that HOXA1-7 are expressed (turned on). We can also see that HOXA9-13 is not expressed (turned off). "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on our course contributors table guidelines.     Credits Names Pedagogy Lead Content Instructor Ifeoma Nwigwe Content Reviewers Elizabeth Humphries, Natalie Kucher Content Director Ava Hoffman Technical Course Publishing Engineer Ava Hoffman Template Publishing Engineers Candace Savonen, Carrie Wright Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Candace Savonen Package Developers (ottrpal) John Muschelli, Candace Savonen, Carrie Wright Funding Funder [National Human Genome Research Institute (NHGRI)] #5U24HG010263 Funding Staff Fallon Bachman, Jennifer Vessio, Emily Voeglein   ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.3.2 (2023-10-31) ## os Ubuntu 22.04.4 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2025-02-04 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) ## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) ## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) ## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) ## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) ## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) ## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) ## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) ## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) ## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) ## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) ## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) ## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) ## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2) ## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) ## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) ## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) ## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) ## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) ## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) ## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) ## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) ## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) ## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) ## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) ## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) ## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) ## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0) ## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0) ## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) ## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) ## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) ## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) ## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library ## ## ────────────────────────────────────────────────────────────────────────────── "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). 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