{"id":6362,"date":"2022-04-19T14:34:43","date_gmt":"2022-04-19T18:34:43","guid":{"rendered":"https:\/\/sites.miamioh.edu\/undergraduate-research-forum\/?p=6362"},"modified":"2022-04-21T11:17:03","modified_gmt":"2022-04-21T15:17:03","slug":"b41-comparing-atac-seg-and-rna-seg-data-to-understand-how-chromatin-accessibility-and-gene-expression-correlate-in-differentiating-lens-epithelial-cells","status":"publish","type":"post","link":"https:\/\/sites.miamioh.edu\/undergraduate-research-forum\/b41-comparing-atac-seg-and-rna-seg-data-to-understand-how-chromatin-accessibility-and-gene-expression-correlate-in-differentiating-lens-epithelial-cells\/","title":{"rendered":"B41: Comparing ATAC-seq and RNA-seq Data to Understand How Chromatin Accessibility and Gene Expression Correlate in Differentiating Lens Epithelial Cells"},"content":{"rendered":"\n

This project focuses on lens cells by analyzing the genetic changes that happen as lens epithelial cells differentiate into lens fiber cells and how these changes correlate to gene expression. The main question I am asking in this project is how does the accessibility of chromatin relate to the expression of genes in differentiating lens epithelial cells. In order to study the genes that are both accessible to expression machinery and expressed in these cells, several lens epithelial explants were made. This method allows us to study only the lens epithelium, and also allows us to culture the epithelium in different media, such as vitreous. Vitreous is the substance found between the lens and the retina in eyes, and is known to induce differentiation in lens cells. After the explants are prepared, we can extract the DNA and perform ATAC-seq analysis on the samples. For this study, we did this under three different conditions: immediately after creating the explant, after one day of culture in media, and after one day of culture in vitreous. Based on the data collected, I was able to correlate the differentially accessible regions (DARs) from the ATAC-seq data with the differentially expressed genes (GEGs), from previously collected RNA-seq data. From this analysis, I am able to conclude that in differentiating lens epithelial cells, increased accessibility positively correlates with increased gene expression. Meaning that if a gene is expressed in a differentiating lens epithelial cell, it is also accessible to the enzymes that aid in gene expression. This experience is relevant to my intended career because it has allowed me to gain experience working in a lab as well as allowing me to learn new and relevant techniques in genetic analysis.<\/p>\n\n\n\n

Author: Raye Palko<\/p>\n\n\n\n

Advisor: Michael L. Robinson, Biology<\/p>\n\n\n\n

Graduate Advisor: Anil Upreti, Biology<\/p>\n\n\n\n

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This project focuses on lens cells by analyzing the genetic changes that happen as lens epithelial cells differentiate into lens fiber cells and how these changes correlate to gene expression. The main question I am asking in this project is how does the accessibility of chromatin relate to the expression of genes in differentiating lens […]<\/p>\n","protected":false},"author":301,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_bbp_topic_count":0,"_bbp_reply_count":0,"_bbp_total_topic_count":0,"_bbp_total_reply_count":0,"_bbp_voice_count":0,"_bbp_anonymous_reply_count":0,"_bbp_topic_count_hidden":0,"_bbp_reply_count_hidden":0,"_bbp_forum_subforum_count":0,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[924,1,936,24],"tags":[1126,1125,618,89],"class_list":["post-6362","post","type-post","status-publish","format-standard","hentry","category-2022-talks","category-projects","category-b34-44","category-biology","tag-differentiation","tag-lens","tag-microbiology","tag-stem"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/pbRpLx-1EC","jetpack_likes_enabled":true,"_links":{"self":[{"href":"https:\/\/sites.miamioh.edu\/undergraduate-research-forum\/wp-json\/wp\/v2\/posts\/6362","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.miamioh.edu\/undergraduate-research-forum\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/sites.miamioh.edu\/undergraduate-research-forum\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/sites.miamioh.edu\/undergraduate-research-forum\/wp-json\/wp\/v2\/users\/301"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.miamioh.edu\/undergraduate-research-forum\/wp-json\/wp\/v2\/comments?post=6362"}],"version-history":[{"count":0,"href":"https:\/\/sites.miamioh.edu\/undergraduate-research-forum\/wp-json\/wp\/v2\/posts\/6362\/revisions"}],"wp:attachment":[{"href":"https:\/\/sites.miamioh.edu\/undergraduate-research-forum\/wp-json\/wp\/v2\/media?parent=6362"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/sites.miamioh.edu\/undergraduate-research-forum\/wp-json\/wp\/v2\/categories?post=6362"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/sites.miamioh.edu\/undergraduate-research-forum\/wp-json\/wp\/v2\/tags?post=6362"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}