{"id":263,"date":"2022-04-09T15:37:40","date_gmt":"2022-04-09T15:37:40","guid":{"rendered":"https:\/\/promoter-benchmark.epfl.ch\/?page_id=263"},"modified":"2023-06-27T17:24:14","modified_gmt":"2023-06-27T17:24:14","slug":"faq","status":"publish","type":"page","link":"https:\/\/promoter-benchmark.epfl.ch\/index.php\/faq\/","title":{"rendered":"FAQ"},"content":{"rendered":"

1. Where can I find the inducible transcriptional system library?<\/span><\/p>\n

The plasmids that contain inducible transcriptional systems driving the expression of yEVenus-PEST<\/em> can be obtained from Addgene: https:\/\/www.addgene.org\/browse\/article\/28215792\/<\/a><\/span><\/p>\n

The strains that contain single copies of the reporter constructs can be obtained from National BioResource Project – Yeast database: https:\/\/yeast.nig.ac.jp\/yeast\/by\/StrainAllItemsList.jsf?id=29087-29102<\/a><\/span><\/p>\n

The sequences of the used promoters are available on the promoters’ respective webpages.<\/span><\/p>\n

The raw single-cell data of the transcriptional systems activity are available on the promoter’s respective webpages.<\/span><\/p>\n

2. How can I compare my promoter’s level of expression to the promoters’ from the library?<\/span><\/p>\n

You can start by comparing the level of activity of your promoter to the GAL1pr<\/em> induction in galactose. We introduced an intuitive unit as a measure of promoter’s activity, maxGAL1, which corresponds to average activity of GAL1pr in stationary phase of induction in synthetic complete media containing 3% raffinose and 2% galactose.<\/span><\/p>\n

3. How can I extract the parameters of induction for my promoter to compare it with the ones from the publication?\u00a0<\/span><\/p>\n

You can use our code: https:\/\/github.com\/lpbsscientist\/promoter-benchmark-model<\/a>.<\/span><\/p>\n

4. Where can I find source data from the publication?<\/span><\/p>\n

Here<\/a>, or under ‘download single-cell induction data’ on the webpage of the transcriptional system you’re interested in.<\/span><\/p>\n

5.\u00a0 How is promoters’ activity measured?<\/span><\/p>\n

As a reporter of promoters’ activity, we have used a fast-folding bright fluorescent protein optimized for expression in budding yeast, yEVenus. The fluorescence was measured using fluorescent microscopy, by tracking the levels of yEVenus-PEST around and during a 3.5 h induction. The microscopy data was analyzed using YeaZ, a neural-network based tool for segmentation of yeast microscopy images (Dietler, N., Minder, M., Gligorovski, V. et al. A convolutional neural network segments yeast microscopy images with high accuracy. Nat Commun 11, 5723 (2020). https:\/\/doi.org\/10.1038\/s41467-020-19557-4<\/a>)<\/span><\/p>\n

5. How are promoters in the library standardized?<\/span><\/p>\n

To allow direct comparison between the promoters in the library, we designed the budding yeast strains harboring different promoters to be the same in terms of:<\/span>
\n– integration locus: all reportes are integrated in the URA3<\/em> locus<\/span>
\n– copy number: all reportes are integrated in single copies<\/span>
\n– the plasmids backbone used as a starting point for cloning<\/span>
\n– the sequence between the promoter and the yEVenus<\/em> reporter<\/span><\/p>\n

6. I found an error on the website, who can I contact?<\/span><\/p>\n

For any suggestions or comments about the website, or in case you find any errors, please write to Vojislav Gligorovski<\/a>.<\/span><\/p>\n

7. \u00a0How to cite us?<\/span><\/p>\n

If you have used the inducible promoters library characterization for designing your experiments, please cite the following manuscript:<\/span>
\nGligorovski, V., Sadeghi, A. & Rahi, S.J. Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor. Nat Commun 14, 3810 (2023). https:\/\/doi.org\/10.1038\/s41467-023-38959-8<\/a><\/span><\/p>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

1. Where can I find the inducible transcriptional system library? The plasmids that contain inducible transcriptional systems driving the expression of yEVenus-PEST can be obtained from Addgene: https:\/\/www.addgene.org\/browse\/article\/28215792\/ The strains that contain single copies of the reporter constructs can be obtained from National BioResource Project – Yeast database: https:\/\/yeast.nig.ac.jp\/yeast\/by\/StrainAllItemsList.jsf?id=29087-29102 The sequences of the used promoters […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ocean_post_layout":"","ocean_both_sidebars_style":"","ocean_both_sidebars_content_width":0,"ocean_both_sidebars_sidebars_width":0,"ocean_sidebar":"0","ocean_second_sidebar":"0","ocean_disable_margins":"enable","ocean_add_body_class":"","ocean_shortcode_before_top_bar":"","ocean_shortcode_after_top_bar":"","ocean_shortcode_before_header":"","ocean_shortcode_after_header":"","ocean_has_shortcode":"","ocean_shortcode_after_title":"","ocean_shortcode_before_footer_widgets":"","ocean_shortcode_after_footer_widgets":"","ocean_shortcode_before_footer_bottom":"","ocean_shortcode_after_footer_bottom":"","ocean_display_top_bar":"default","ocean_display_header":"default","ocean_header_style":"","ocean_center_header_left_menu":"0","ocean_custom_header_template":"0","ocean_custom_logo":0,"ocean_custom_retina_logo":0,"ocean_custom_logo_max_width":0,"ocean_custom_logo_tablet_max_width":0,"ocean_custom_logo_mobile_max_width":0,"ocean_custom_logo_max_height":0,"ocean_custom_logo_tablet_max_height":0,"ocean_custom_logo_mobile_max_height":0,"ocean_header_custom_menu":"0","ocean_menu_typo_font_family":"0","ocean_menu_typo_font_subset":"","ocean_menu_typo_font_size":0,"ocean_menu_typo_font_size_tablet":0,"ocean_menu_typo_font_size_mobile":0,"ocean_menu_typo_font_size_unit":"px","ocean_menu_typo_font_weight":"","ocean_menu_typo_font_weight_tablet":"","ocean_menu_typo_font_weight_mobile":"","ocean_menu_typo_transform":"","ocean_menu_typo_transform_tablet":"","ocean_menu_typo_transform_mobile":"","ocean_menu_typo_line_height":0,"ocean_menu_typo_line_height_tablet":0,"ocean_menu_typo_line_height_mobile":0,"ocean_menu_typo_line_height_unit":"","ocean_menu_typo_spacing":0,"ocean_menu_typo_spacing_tablet":0,"ocean_menu_typo_spacing_mobile":0,"ocean_menu_typo_spacing_unit":"","ocean_menu_link_color":"","ocean_menu_link_color_hover":"","ocean_menu_link_color_active":"","ocean_menu_link_background":"","ocean_menu_link_hover_background":"","ocean_menu_link_active_background":"","ocean_menu_social_links_bg":"","ocean_menu_social_hover_links_bg":"","ocean_menu_social_links_color":"","ocean_menu_social_hover_links_color":"","ocean_disable_title":"default","ocean_disable_heading":"default","ocean_post_title":"","ocean_post_subheading":"","ocean_post_title_style":"","ocean_post_title_background_color":"","ocean_post_title_background":0,"ocean_post_title_bg_image_position":"","ocean_post_title_bg_image_attachment":"","ocean_post_title_bg_image_repeat":"","ocean_post_title_bg_image_size":"","ocean_post_title_height":0,"ocean_post_title_bg_overlay":0.5,"ocean_post_title_bg_overlay_color":"","ocean_disable_breadcrumbs":"default","ocean_breadcrumbs_color":"","ocean_breadcrumbs_separator_color":"","ocean_breadcrumbs_links_color":"","ocean_breadcrumbs_links_hover_color":"","ocean_display_footer_widgets":"default","ocean_display_footer_bottom":"default","ocean_custom_footer_template":"0","footnotes":""},"class_list":["post-263","page","type-page","status-publish","hentry","entry"],"featured_image_src":null,"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/promoter-benchmark.epfl.ch\/index.php\/wp-json\/wp\/v2\/pages\/263","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/promoter-benchmark.epfl.ch\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/promoter-benchmark.epfl.ch\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/promoter-benchmark.epfl.ch\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/promoter-benchmark.epfl.ch\/index.php\/wp-json\/wp\/v2\/comments?post=263"}],"version-history":[{"count":0,"href":"https:\/\/promoter-benchmark.epfl.ch\/index.php\/wp-json\/wp\/v2\/pages\/263\/revisions"}],"wp:attachment":[{"href":"https:\/\/promoter-benchmark.epfl.ch\/index.php\/wp-json\/wp\/v2\/media?parent=263"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}