BAC resources - Revision history

Xenbase at 15:02, 6 October 2023

2023-10-06T15:02:21Z

← Older revision		Revision as of 15:02, 6 October 2023
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	A subset of the ''S. purpuratus'' BACs have been mapped to the genome assembly. As part of the SUGP, about 8,000 BAC clones were end sequenced using Sanger technology. Genomic positions for these BACs are indicated as a track in JBrowse (link). An additional set of individual BACs were sequenced completely; links to the NCBI page is provided for these. Finally, some BACs have been identified using hybridization screening of arrayed library filters (see [[BAC_Table\|BAC Table ]]).		A subset of the ''S. purpuratus'' BACs have been mapped to the genome assembly. As part of the SUGP, about 8,000 BAC clones were end sequenced using Sanger technology. Genomic positions for these BACs are indicated as a track in JBrowse (link). An additional set of individual BACs were sequenced completely; links to the NCBI page is provided for these. Finally, some BACs have been identified using hybridization screening of arrayed library filters (see [[BAC_Table\|BAC Table ]]).

	'''BAC Vector Sequence'''. The BACs are maintained in the [https://bacpacresources.org/pbace36.htm pBACe3.6 vector] which originates from Children's Hospital Oakland Research Institute in Oakland, California, USA. This vector confers resistance to the antibiotic chloramphenicol and is fully described by <span class="newwin">[http://~~new~~.echinobase.org/literature/article.do?method=display&articleId=48450 Frengen and colleages]</span>. The vector sequence is available [http://www.ncbi.nlm.nih.gov/nuccore/4878025?report=fasta here].		'''BAC Vector Sequence'''. The BACs are maintained in the [https://bacpacresources.org/pbace36.htm pBACe3.6 vector] which originates from Children's Hospital Oakland Research Institute in Oakland, California, USA. This vector confers resistance to the antibiotic chloramphenicol and is fully described by <span class="newwin">[http://www.echinobase.org/literature/article.do?method=display&articleId=48450 Frengen and colleages]</span>. The vector sequence is available [http://www.ncbi.nlm.nih.gov/nuccore/4878025?report=fasta here].

	'''Relevant publications:'''<br />		'''Relevant publications:'''<br />
	<span class="newwin">[http://~~new~~.echinobase.org/literature/article.do?method=display&articleId=37498 A sea urchin genome project: Sequence scan, virtual map, and additional resources. Cameron, RA, et al., 2000. Proc. Natl. Acad. Sci. USA.]</span><br />		<span class="newwin">[http://www.echinobase.org/literature/article.do?method=display&articleId=37498 A sea urchin genome project: Sequence scan, virtual map, and additional resources. Cameron, RA, et al., 2000. Proc. Natl. Acad. Sci. USA.]</span><br />
	<span class="newwin">[http://~~new~~.echinobase.org/literature/article.do?method=display&articleId=45819 Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms. Buckley, KM et al., 2017. Briefings in Functional Genomics]</span>.		<span class="newwin">[http://www.echinobase.org/literature/article.do?method=display&articleId=45819 Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms. Buckley, KM et al., 2017. Briefings in Functional Genomics]</span>.

	== BAC Protocols ==		== BAC Protocols ==
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	'''To request a recombinant or wildtype BAC for non-commercial use:'''<br />		'''To request a recombinant or wildtype BAC for non-commercial use:'''<br />
	1. Identify the BAC of interest computationally or by screening our libraries ([[filters]]).<br />		1. Identify the BAC of interest computationally or by screening our libraries ([[filters]]).<br />
	2. Request the BAC by emailing [mailto:ctelmer@cmu.edu Cheryl Telmer] or <span class="newwin">[http://~~new~~.echinobase.org/community/person.do?method=display&personId=4136&tabId=0 Veronica Hinman]</span>.		2. Request the BAC by emailing [mailto:ctelmer@cmu.edu Cheryl Telmer] or <span class="newwin">[http://www.echinobase.org/community/person.do?method=display&personId=4136&tabId=0 Veronica Hinman]</span>.

	<br />		<br />

imported>Ctelmer: /* Recombinant BAC Resources */

2020-04-17T21:27:36Z

Recombinant BAC Resources

← Older revision		Revision as of 21:27, 17 April 2020
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	'''To request a recombinant or wildtype BAC for non-commercial use:'''<br />		'''To request a recombinant or wildtype BAC for non-commercial use:'''<br />
	1. Identify the BAC of interest computationally or by screening our libraries ([[filters]]).<br />		1. Identify the BAC of interest computationally or by screening our libraries ([[filters]]).<br />
	2. Request the BAC by emailing [mailto:~~kbuckle2~~@~~andrew.~~cmu.edu ~~Kate Buckley~~] or <span class="newwin">[http://new.echinobase.org/community/person.do?method=display&personId=4136&tabId=0 Veronica Hinman]</span>.		2. Request the BAC by emailing [mailto:ctelmer@cmu.edu Cheryl Telmer] or <span class="newwin">[http://new.echinobase.org/community/person.do?method=display&personId=4136&tabId=0 Veronica Hinman]</span>.

	<br />		<br />

imported>Echinobase: /* Genomic BAC Resources */

2020-02-13T00:43:15Z

Genomic BAC Resources

← Older revision		Revision as of 00:43, 13 February 2020
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	A subset of the ''S. purpuratus'' BACs have been mapped to the genome assembly. As part of the SUGP, about 8,000 BAC clones were end sequenced using Sanger technology. Genomic positions for these BACs are indicated as a track in JBrowse (link). An additional set of individual BACs were sequenced completely; links to the NCBI page is provided for these. Finally, some BACs have been identified using hybridization screening of arrayed library filters (see [[BAC_Table\|BAC Table ]]).		A subset of the ''S. purpuratus'' BACs have been mapped to the genome assembly. As part of the SUGP, about 8,000 BAC clones were end sequenced using Sanger technology. Genomic positions for these BACs are indicated as a track in JBrowse (link). An additional set of individual BACs were sequenced completely; links to the NCBI page is provided for these. Finally, some BACs have been identified using hybridization screening of arrayed library filters (see [[BAC_Table\|BAC Table ]]).

	'''BAC Vector Sequence'''. The BACs are maintained in the [~~http~~://~~bacpac.chori~~.org/pbace36.htm pBACe3.6 vector] which originates from Children's Hospital Oakland Research Institute in Oakland, California, USA. This vector confers resistance to the antibiotic chloramphenicol and is fully described by [http://~~www~~.~~ncbi~~.~~nlm.nih.gov~~/~~pubmed~~/~~10373322~~?~~dopt~~=~~Abstract~~ Frengen and colleages]. The vector sequence is available [http://www.ncbi.nlm.nih.gov/nuccore/4878025?report=fasta here].		'''BAC Vector Sequence'''. The BACs are maintained in the [https://bacpacresources.org/pbace36.htm pBACe3.6 vector] which originates from Children's Hospital Oakland Research Institute in Oakland, California, USA. This vector confers resistance to the antibiotic chloramphenicol and is fully described by <span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=48450 Frengen and colleages]</span>. The vector sequence is available [http://www.ncbi.nlm.nih.gov/nuccore/4878025?report=fasta here].

	'''Relevant publications:'''<br />		'''Relevant publications:'''<br />
	[http://~~www~~.~~pnas~~.org/~~content/97~~/~~17/9514~~.~~full~~ A sea urchin genome project: Sequence scan, virtual map, and additional resources.] Cameron, RA, et al., 2000. Proc. Natl. Acad. Sci. USA.<br />		<span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=37498 A sea urchin genome project: Sequence scan, virtual map, and additional resources. Cameron, RA, et al., 2000. Proc. Natl. Acad. Sci. USA.]</span><br />
	[~~[LINK~~. Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms.]] Buckley, KM et al., 2017. Briefings in Functional Genomics.		<span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=45819 Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms. Buckley, KM et al., 2017. Briefings in Functional Genomics]</span>.

	== BAC Protocols ==		== BAC Protocols ==

imported>Echinobase: /* Genomic BAC Resources */

2020-02-13T00:36:20Z

Genomic BAC Resources

← Older revision		Revision as of 00:36, 13 February 2020
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	== Genomic BAC Resources ==		== Genomic BAC Resources ==

	Echinobase stores libraries of genomic sequence fragments maintained in bacterial artificial chromosome (BAC) vectors for seven lower deuterostome species [[~~Echinobase/bac_table/bac_table.php~~\|~~'''(~~BAC Table~~)'''~~]]. These libraries were originally constructed as part of the Sea Urchin Genome Project. On average, the insert sizes for our BAC libraries are ~140 kb. Thus, for the 800 Mb ''S. purpuratus'' genome, 1X coverage is encompassed by, on average, 5,700 clones. Each library consists of >100,000 clones, providing ~17X genome coverage.		Echinobase stores libraries of genomic sequence fragments maintained in bacterial artificial chromosome (BAC) vectors for seven lower deuterostome species [[BAC_Table\|BAC Table]]. These libraries were originally constructed as part of the Sea Urchin Genome Project. On average, the insert sizes for our BAC libraries are ~140 kb. Thus, for the 800 Mb ''S. purpuratus'' genome, 1X coverage is encompassed by, on average, 5,700 clones. Each library consists of >100,000 clones, providing ~17X genome coverage.

	A subset of the ''S. purpuratus'' BACs have been mapped to the genome assembly. As part of the SUGP, about 8,000 BAC clones were end sequenced using Sanger technology. Genomic positions for these BACs are indicated as a track in JBrowse (link). An additional set of individual BACs were sequenced completely; links to the NCBI page is provided for these. Finally, some BACs have been identified using hybridization screening of arrayed library filters (see [[~~Echinobase/bac_table/bac_table.php~~\|~~'''(~~BAC Table~~)'''~~]])		A subset of the ''S. purpuratus'' BACs have been mapped to the genome assembly. As part of the SUGP, about 8,000 BAC clones were end sequenced using Sanger technology. Genomic positions for these BACs are indicated as a track in JBrowse (link). An additional set of individual BACs were sequenced completely; links to the NCBI page is provided for these. Finally, some BACs have been identified using hybridization screening of arrayed library filters (see [[BAC_Table\|BAC Table ]]).

	'''BAC Vector Sequence'''. The BACs are maintained in the [http://bacpac.chori.org/pbace36.htm pBACe3.6 vector] which originates from Children's Hospital Oakland Research Institute in Oakland, California, USA. This vector confers resistance to the antibiotic chloramphenicol and is fully described by [http://www.ncbi.nlm.nih.gov/pubmed/10373322?dopt=Abstract Frengen and colleages]. The vector sequence is available [http://www.ncbi.nlm.nih.gov/nuccore/4878025?report=fasta here].		'''BAC Vector Sequence'''. The BACs are maintained in the [http://bacpac.chori.org/pbace36.htm pBACe3.6 vector] which originates from Children's Hospital Oakland Research Institute in Oakland, California, USA. This vector confers resistance to the antibiotic chloramphenicol and is fully described by [http://www.ncbi.nlm.nih.gov/pubmed/10373322?dopt=Abstract Frengen and colleages]. The vector sequence is available [http://www.ncbi.nlm.nih.gov/nuccore/4878025?report=fasta here].
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	[http://www.pnas.org/content/97/17/9514.full A sea urchin genome project: Sequence scan, virtual map, and additional resources.] Cameron, RA, et al., 2000. Proc. Natl. Acad. Sci. USA.<br />		[http://www.pnas.org/content/97/17/9514.full A sea urchin genome project: Sequence scan, virtual map, and additional resources.] Cameron, RA, et al., 2000. Proc. Natl. Acad. Sci. USA.<br />
	[[LINK. Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms.]] Buckley, KM et al., 2017. Briefings in Functional Genomics.		[[LINK. Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms.]] Buckley, KM et al., 2017. Briefings in Functional Genomics.



	== BAC Protocols ==		== BAC Protocols ==

imported>Echinobase: /* Recombinant BAC Resources */

2020-02-13T00:35:17Z

Recombinant BAC Resources

← Older revision		Revision as of 00:35, 13 February 2020
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	== Recombinant BAC Resources ==		== Recombinant BAC Resources ==

	Echinobase has generated and maintains a set of reporter BAC constructs in which a portion of the gene of interest is replaced by the sequence encoding a fluorescent protein (''i.e.'' GFP, mCherry). A list of these sequences is available [[~~Echinobase/bac_table/bac_table.php~~\|~~'''~~here~~'''~~]]). Existing clones are available by request. We will also consider requests to make additional recombinant reporter constructs as time permits.		Echinobase has generated and maintains a set of reporter BAC constructs in which a portion of the gene of interest is replaced by the sequence encoding a fluorescent protein (''i.e.'' GFP, mCherry). A list of these sequences is available [[BAC_Table\|here]]). Existing clones are available by request. We will also consider requests to make additional recombinant reporter constructs as time permits.

	'''To request a recombinant or wildtype BAC for non-commercial use:'''<br />		'''To request a recombinant or wildtype BAC for non-commercial use:'''<br />
	1. Identify the BAC of interest computationally or by screening our libraries ([[filters]]).<br />		1. Identify the BAC of interest computationally or by screening our libraries ([[filters]]).<br />
	2. Request the BAC by emailing [mailto:kbuckle2@andrew.cmu.edu Kate Buckley] or [~~mailto~~:~~veronica@cmu~~.~~edu~~ Veronica Hinman].		2. Request the BAC by emailing [mailto:kbuckle2@andrew.cmu.edu Kate Buckley] or <span class="newwin">[http://new.echinobase.org/community/person.do?method=display&personId=4136&tabId=0 Veronica Hinman]</span>.

	<br />		<br />

imported>Echinobase: /* Recombinant BAC Resources */

2020-02-13T00:32:26Z

Recombinant BAC Resources

← Older revision		Revision as of 00:32, 13 February 2020
Line 29:		Line 29:

	'''To request a recombinant or wildtype BAC for non-commercial use:'''<br />		'''To request a recombinant or wildtype BAC for non-commercial use:'''<br />
	1. Identify the BAC of interest computationally or by screening our libraries ([[~~Echinobase/filters\|available~~ filters]]).<br />		1. Identify the BAC of interest computationally or by screening our libraries ([[filters]]).<br />
	2. Request the BAC by emailing [mailto:kbuckle2@andrew.cmu.edu Kate Buckley] or [mailto:veronica@cmu.edu Veronica Hinman].		2. Request the BAC by emailing [mailto:kbuckle2@andrew.cmu.edu Kate Buckley] or [mailto:veronica@cmu.edu Veronica Hinman].

imported>Echinobase: /* Recombinant BAC Resources */

2020-02-13T00:31:23Z

Recombinant BAC Resources

← Older revision		Revision as of 00:31, 13 February 2020
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	[[File:~~/Echinobase/sites/default/files/~~Bac.jpg\|~~navigation~~]]		[[File:Bac.jpg\|600px]]


	== Working with BACs ==		== Working with BACs ==

imported>Echinobase: Created page with " == Genomic BAC Resources == Echinobase stores libraries of genomic sequence fragments maintained in bacterial artificial chromosome (BAC) vectors for seven lower deuterostom..."

2020-02-12T21:44:23Z

Created page with " == Genomic BAC Resources == Echinobase stores libraries of genomic sequence fragments maintained in bacterial artificial chromosome (BAC) vectors for seven lower deuterostom..."

New page

== Genomic BAC Resources ==

Echinobase stores libraries of genomic sequence fragments maintained in bacterial artificial chromosome (BAC) vectors for seven lower deuterostome species [[Echinobase/bac_table/bac_table.php|'''(BAC Table)''']]. These libraries were originally constructed as part of the Sea Urchin Genome Project. On average, the insert sizes for our BAC libraries are ~140 kb. Thus, for the 800 Mb ''S. purpuratus'' genome, 1X coverage is encompassed by, on average, 5,700 clones. Each library consists of >100,000 clones, providing ~17X genome coverage.

A subset of the ''S. purpuratus'' BACs have been mapped to the genome assembly. As part of the SUGP, about 8,000 BAC clones were end sequenced using Sanger technology. Genomic positions for these BACs are indicated as a track in JBrowse (link). An additional set of individual BACs were sequenced completely; links to the NCBI page is provided for these. Finally, some BACs have been identified using hybridization screening of arrayed library filters (see [[Echinobase/bac_table/bac_table.php|'''(BAC Table)''']])

'''BAC Vector Sequence'''. The BACs are maintained in the [http://bacpac.chori.org/pbace36.htm pBACe3.6 vector] which originates from Children's Hospital Oakland Research Institute in Oakland, California, USA. This vector confers resistance to the antibiotic chloramphenicol and is fully described by [http://www.ncbi.nlm.nih.gov/pubmed/10373322?dopt=Abstract Frengen and colleages]. The vector sequence is available [http://www.ncbi.nlm.nih.gov/nuccore/4878025?report=fasta here].

'''Relevant publications:''' 
[http://www.pnas.org/content/97/17/9514.full A sea urchin genome project: Sequence scan, virtual map, and additional resources.] Cameron, RA, et al., 2000. Proc. Natl. Acad. Sci. USA. 
[[LINK. Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms.]] Buckley, KM et al., 2017. Briefings in Functional Genomics.

== BAC Protocols ==

Screening a BAC library 
Generating a recombinant BAC 
BAC miniprep protocol 
Analyzing BAC DNA by PFGE

 

== Recombinant BAC Resources ==

Echinobase has generated and maintains a set of reporter BAC constructs in which a portion of the gene of interest is replaced by the sequence encoding a fluorescent protein (''i.e.'' GFP, mCherry). A list of these sequences is available [[Echinobase/bac_table/bac_table.php|'''here''']]). Existing clones are available by request. We will also consider requests to make additional recombinant reporter constructs as time permits.

'''To request a recombinant or wildtype BAC for non-commercial use:''' 
1. Identify the BAC of interest computationally or by screening our libraries ([[Echinobase/filters|available filters]]). 
2. Request the BAC by emailing [mailto:kbuckle2@andrew.cmu.edu Kate Buckley] or [mailto:veronica@cmu.edu Veronica Hinman].

 

[[File:/Echinobase/sites/default/files/Bac.jpg|navigation]]

== Working with BACs ==

'''Storing BACs'''

'''Short term''' 
To avoid shearing the long BAC DNA fragments, ''isolated BACs should never be vortexed or frozen''. Store BAC DNA at 4 C in TE (10 mM Tris, pH = 7.4; 10 mM EDTA). 
'''Long term storage''' 
Store glycerol bacteria stocks (15-25% glycerol) at -80 C.

'''Antibiotic conditions for working with BAC clones''' 
'''Kanamycin''' 
Stock (25 μg/μL): Dissolve 0.5 g of kanamycin into 10 ml of ddH2O. Filter through a 0.22 µm filter to sterilize. Aliquot and store at -20°C. 
Use at 1:1000 dilution (25 μg/mL). 
'''Chloramphenicol''' 
Stock (25 μg/μl): Dissolve in ETOH store at -20. 
Use at 1:2000 dilution.(12.5 μg/ml)