{"id":3960,"date":"2015-01-14T14:30:33","date_gmt":"2015-01-14T05:30:33","guid":{"rendered":"http:\/\/dna1.dna.rbrc.jp\/en\/?page_id=3960"},"modified":"2023-06-09T16:57:23","modified_gmt":"2023-06-09T07:57:23","slug":"manualen","status":"publish","type":"page","link":"http:\/\/dna.brc.riken.jp\/en\/manualen","title":{"rendered":"Lab Manual"},"content":{"rendered":"<h1>Lab Manual<\/h1>\n<h2>Protocol<\/h2>\n<h3>Handling of genetic materials<\/h3>\n<ul style=\"line-height: 1.5em;\">\n<li>Stab culture\n<ul style=\"line-height: 1.5em;\">\n<li>Inoculate the bacteria on an agar plate containing appropriate selective antibiotics and\/or nutritional supplements within a few days after you received the plastic vial of stab culture.<\/li>\n<li>Pick up bacteria from the middle part of stab culture but not those from the surface of the stab which are not really healthy.<\/li>\n<li>CAUTION: The vial should be placed in a refrigerator (4&deg;C) but never in a freezer, otherwise spoiled.<br \/>\n<img decoding=\"async\" alt=\"\" src=\"https:\/\/dnaconda.riken.jp\/images\/strain.gif\"><\/li>\n<\/ul>\n<\/li>\n<li><a href=\"https:\/\/brc.riken.jp\/dna\/MAN0001e\">BAC Related Information<\/a><\/li>\n<li><a href=\"https:\/\/brc.riken.jp\/dna\/MAN0007e\">Microbe Genomic DNA Preparation<\/a><\/li>\n<li><a href=\"https:\/\/cfm.brc.riken.jp\/lentiviral-vectors\/protocols\/\">Lentiviral vectors [link]<\/a><\/li>\n<\/ul>\n<h3>Sequencing &amp; PCR primer<\/h3>\n<ul style=\"line-height: 1.5em;\">\n<li><a href=\"https:\/\/brc.riken.jp\/dna\/MAN0035e\">Sequencing &amp; PCR primers<\/a><\/li>\n<li><a href=\"https:\/\/brc.riken.jp\/dna\/MAN0007e\">Primers for PCR of rRNA gene (Microbe Genomic DNA Information)<\/a><\/li>\n<li><a href=\"https:\/\/dnaconda.riken.jp\/rvd\/stsmkr.html\">List of STS Markers for Detection of Virus Genes<\/a><\/li>\n<\/ul>\n<h3>Protocol by using deposited matelials<\/h3>\n<ul style=\"line-height: 1.5em;\">\n<li><span style=\"text-decoration:underline;\">Expression and Purification of Recombinant Galectins<\/span><br \/>\n<table>\n<tbody>\n<tr>\n<th>Resource page<\/th>\n<th>Protocol<\/th>\n<\/tr>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/GSB0048e\">Lectin (GSB0048) &#8211; Gene Set Collection<\/a><\/td>\n<td>Nishi, H. A note on expression and purification of recombinant galectins. Glycoforum Vol.23 (5), A15 (2020). DOI: https:\/\/doi.org\/10.32285\/glycoforum.23A15.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<li><span style=\"text-decoration:underline;\"><a href=\"https:\/\/brc.riken.jp\/dna\/MAN0020e\">Purification of Recombinant Tubulin by Dr. Etsuko Muto [pdf]<\/a><\/span><br \/>\n<table>\n<tbody>\n<tr>\n<th>Catalog #<\/th>\n<th>Resource name<\/th>\n<th>Description<\/th>\n<tr>\n<td>RDB12753<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB12753\">pFBD-Hs alpha1CGH\/beta3CGF<\/a><\/td>\n<td>Plasmid clone for baculoviral expression of alpha1 and beta3 tubulin.<\/td>\n<\/tr>\n<tr>\n<td>RDB12754<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB12754\">pFBD-Hs alpha1(K40R)CGH\/beta3CGF<\/a><\/td>\n<td>Plasmid clone for baculoviral expression of alpha1 and beta3 tubulin.<\/td>\n<\/tr>\n<tr>\n<td>RDB14530<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB14530\">pFBD-Hs alpha1 CFXaGH\/beta3 CFXaGF<\/a><\/td>\n<td>Expression vector of His tagged human tubulin alpha-1and Flag tagged human tubulin beta-3.<\/td>\n<\/tr>\n<tr>\n<td>RDB14531<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB14531\">pFBD-Hs alpha1(K40R) CFXaGH\/beta3 CFXaGF<\/a><\/td>\n<td>Expression vector of His tagged human tubulin alpha-1(mutant, K40R, constitutive active form) and Flag tagged human tubulin beta-3.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<li><span style=\"text-decoration:underline;\">Expression of heterologous proteins in Drosophila Schneider S2 (S2)<\/span><br \/>\n<table>\n<tbody>\n<tr>\n<th>Resource page<\/th>\n<th>Protocol<\/th>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/GRP0048e#insect\">Empty Backbone for Insect Cell Experiment<\/a><\/td>\n<td>A single plasmid transfection that offers a significant advantage associated with puromycin selection in Drosophila Schneider S2 cells expressing heterologous proteins.<br \/>\nIwaki, T., Castellino, F.J.<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=19003171\">Cytotechnology 57 (1), 45-49, (2008). PubMed PMID 19003171.<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<li><span style=\"text-decoration:underline;\">Fluorescence in situ hybridization using bacterial artificial chromosome (BAC) clones<\/span><br \/>\n<table>\n<tbody>\n<tr>\n<th>Resource page<\/th>\n<th>Protocol<\/th>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB13444\">Chinese hamster genomic BAC library clone<\/a><\/td>\n<td>Fluorescence in situ hybridization using bacterial artificial chromosome (BAC) clones for the analysis of chromosome rearrangement in Chinese hamster ovary cells.<br \/>\nCao, Y., Kimura, S., Itoi, T., Honda, K., Ohtake, H., Omasa, T.<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=22100493\">Methods 56 (3): 418-423 (2012). PubMed PMID 22100493.<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<li><span style=\"text-decoration:underline;\">Visualization of sphingolipids<\/span><br \/>\n<table>\n<tbody>\n<tr>\n<th>Resource page<\/th>\n<th>Protocol<\/th>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/GSB0027e\">Genes involved in the sphingolipid signaling pathway<\/a><\/td>\n<td>Dynamics of sphingomyelin-and cholesterol-enriched lipid domains during cytokinesis.<br \/>\nAbe, M., Kobayashi, T.<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=28065303\">Methods Cell Biol. 137: 15-24  (2017). PubMed PMID 28065303.<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<li><span style=\"text-decoration:underline;\">Optogenetic technology using cultured cell lines<\/span><br \/>\n<table>\n<tbody>\n<tr>\n<th>Resource page<\/th>\n<th>Protocol<\/th>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/GRP0057e\">Genetic Resources for Optgenetics Research<\/a><\/td>\n<td>Myogenic Maturation by Optical-Training in Cultured Skeletal Muscle Cells.<br \/>\nAsano, T., Ishizuka, T., Yawo, H.<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=28842907\">Methods Mol. Biol. 1668: 135-145 (2017). PubMed PMID 28842907.<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<li><span style=\"text-decoration:underline;\">Cell-free protein synthesis with noncanonical amino acids using Escherichia coli cell extract<\/span><br \/>\n<table>\n<tbody>\n<tr>\n<th>Resource page<\/th>\n<th>Protocol<\/th>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/GRP0028e#grp0028e\">E. coli strain for producing recombinant proteins incorporating synthetic amino acids<\/a><\/td>\n<td>Cell-Free Protein Synthesis for Multiple Site-Specific Incorporation of Noncanonical Amino Acids Using Cell Extracts from RF-1 Deletion E. coli Strains.<br \/>\nSeki, E., Yanagisawa, T., Yokoyama, S.<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=29404990\">Methods Mol. Biol. 1728: 49-65 (2018). PubMed PMID 29404990.<\/a><\/td>\n<\/tr>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<li><span style=\"text-decoration:underline;\">Cell cycle observation by using Fluorescence Ubiquitination Cell Cycle Indicator (Fucci)<\/span><br \/>\n<table>\n<tbody>\n<tr>\n<th>Resource page<\/th>\n<th>Protocol<\/th>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/GRP0044e\">Fucci &#8211; Fluorescent Ubiquitination-based Cell Cycle Indicator<\/a><\/td>\n<td>Methods to study the proliferation and differentiation of cardiac side population (CSP) cells.<br \/>\nSereti, K.I., Oikonomopoulos, A., Unno, K., Liao, R.<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=23807790\">Methods Mol. Biol.  1036: 95-106 (2013). PubMed PMID 23807790.<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<li><span style=\"text-decoration:underline;\">Transduction of gene to fission yeast by pDUAL and pDUAL2 vectors<\/span><br \/>\n<table>\n<tbody>\n<tr>\n<th>Resource page<\/th>\n<th>Protocol<\/th>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/GRP0027e\">Expression Vector Backbone of S. pombe<\/a><\/td>\n<td>Heterologous gene expression by chromosomal integration in fission yeast.<br \/>\nMatsuyama, A., Yoshida, M.<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=22160913\">Methods Mol. Biol. 824: 433-450 (2012). PubMed PMID 22160913.<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<li><span style=\"text-decoration:underline;\">E. coli-based in-cell NMR experiment<\/span><br \/>\n<table>\n<tbody>\n<tr>\n<th>Resource page<\/th>\n<th>Protocol<\/th>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/GRP0051e\">Thermus thermophilus Expression plasmid<\/a><\/td>\n<td>In-cell NMR of intrinsically disordered proteins in prokaryotic cells.<br \/>\nIto, Y., Mikawa, T., Smith, B.O.<br \/>\n<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=22760309\">Methods Mol. Biol., 895: 19-31 (2012). PubMed PMID 22760309.<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ul>\n<h3>Reference of Genetic Materials<\/h3>\n<ul style=\"line-height: 1.5em;\">\n<li>List of <a href=\"\/en\/manualen\/references_en\">references of genetic materials<\/a> (promoters, plasmid vectors and so on).<\/li>\n<li><a href=\"https:\/\/brc.riken.jp\/dna\/GRP0065e\">List of RDB Clones in Publications<\/a><br \/>\nRDB Clones in Publications is a list of scientific journal and patent application in which provided resources of RIKEN BRC DNA Bank were used. When you publish your research results in a scientific journal, please refer to the origin of materials that were provided from RIKEN BRC and used in your research subject. We appreciate your cooperation.<\/li>\n<\/ul>\n<p><img decoding=\"async\" alt=\"\" src=\"https:\/\/dnaconda.riken.jp\/images\/photo05_750.png\" width=\"200\" \/><\/p>\n<p style=\"text-align: right;\">(MAN0000e 2011.01.12 T.M.)<\/p>\n<p style=\"text-align: left;\">2023.06.08<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Lab Manual Protocol Handling of genetic materials Stab culture Inoculate the bacteria on an agar plate containing appropriate selective antibiotics and\/or nutritional supplements within a few days after you received the plastic vial of stab culture. Pick up bacteria from the middle part of stab culture but not those from the surface of the stab which are not really healthy. CAUTION: The vial should be placed in a refrigerator (4&deg;C) but never in a freezer, otherwise spoiled. BAC Related Information Microbe Genomic DNA Preparation Lentiviral vectors [link] Sequencing &amp; PCR primer Sequencing &amp; PCR primers Primers for PCR of rRNA gene (Microbe Genomic DNA Information) List of STS Markers for Detection of Virus Genes Protocol by using deposited matelials Expression and Purification of Recombinant Galectins Resource page Protocol Lectin (GSB0048) &#8211; Gene Set Collection Nishi, H. A note on expression and purification of recombinant galectins. Glycoforum Vol.23 (5), A15 (2020). DOI: https:\/\/doi.org\/10.32285\/glycoforum.23A15. Purification of Recombinant Tubulin by Dr. Etsuko Muto [pdf] Catalog # Resource name Description RDB12753 pFBD-Hs alpha1CGH\/beta3CGF Plasmid clone for baculoviral expression of alpha1 and beta3 tubulin. RDB12754 pFBD-Hs alpha1(K40R)CGH\/beta3CGF Plasmid clone for baculoviral expression of alpha1 and beta3 tubulin. RDB14530 pFBD-Hs alpha1 CFXaGH\/beta3 CFXaGF Expression vector of [&hellip;]<\/p>\n","protected":false},"author":13,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","_seopress_robots_follow":"","_seopress_robots_imageindex":"","_seopress_robots_snippet":"","_seopress_robots_primary_cat":"","_seopress_robots_breadcrumbs":"","_seopress_robots_freeze_modified_date":"","_seopress_robots_custom_modified_date":"","_seopress_robots_canonical":"","_seopress_social_fb_title":"","_seopress_social_fb_desc":"","_seopress_social_fb_img":"","_seopress_social_fb_img_attachment_id":0,"_seopress_social_fb_img_width":0,"_seopress_social_fb_img_height":0,"_seopress_social_twitter_title":"","_seopress_social_twitter_desc":"","_seopress_social_twitter_img":"","_seopress_social_twitter_img_attachment_id":0,"_seopress_social_twitter_img_width":0,"_seopress_social_twitter_img_height":0,"_seopress_redirections_value":"","_seopress_redirections_enabled":"","_seopress_redirections_enabled_regex":"","_seopress_redirections_logged_status":"both","_seopress_redirections_param":"","_seopress_redirections_type":301,"_seopress_analysis_target_kw":"","footnotes":"","_wp_rev_ctl_limit":""},"class_list":["post-3960","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/3960","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/users\/13"}],"replies":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/comments?post=3960"}],"version-history":[{"count":16,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/3960\/revisions"}],"predecessor-version":[{"id":7927,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/3960\/revisions\/7927"}],"wp:attachment":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/media?parent=3960"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}