Echinobase/bac information and ERNA Table: Difference between pages

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===Table of ''S. purpuratus'' Enhancer RNAs (eRNAs)===


== Genomic BAC Resources ==
<p>The data are available for download [http://ftp.echinobase.org/pub/Genomics/Spur5.0/ here].</p>
<p>The Excel file is called "Table of S. purpuratus eRNAs".</p>
<p>The table contains eRNAs mapped to the ''S. purpuratus'' v5.0 genome.</p>


Echinobase stores libraries of genomic sequence fragments maintained in bacterial artificial chromosome (BAC) vectors for seven lower deuterostome species ([https://wiki.echinobase.org/echinowiki/index.php/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.
===What are eRNAs?===


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. An additional set of individual BACs were sequenced completely; links to the NCBI page are provided in the [https://wiki.echinobase.org/echinowiki/index.php/BAC_Table BAC Table]. Finally, some BACs have been identified using hybridization screening of arrayed library filters (see ([https://wiki.echinobase.org/echinowiki/index.php/BAC_Table BAC Table]))
<p>Enhancers are regions of DNA that are involved in regulating gene expression. Unlike promoters, these cis-regulatory elements do not have strict requirements of position or orientation. In 2010, it was discovered that enhancers can be transcribed to produce enhancer RNAs or eRNAs (reviewed by [https://www.echinobase.org/literature/article.do?method=display&articleId=48875 Arnold, Wells and Li, 2019]). The role of eRNAs and the mechanisms involved in the regulation and expression of developmental genes is the subject of active research.</p>
 
'''BAC Vector Sequence.''' The BACs are maintained in the 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 Frengen and colleages. The vector sequence is available [https://wiki.echinobase.org/echinowiki/index.php/Bac_vector_library here].
 
<br>'''Relevant publications:'''
A sea urchin genome project: Sequence scan, virtual map, and additional resources. [http://www.pnas.org/content/97/17/9514.full Cameron, RA, et al., 2000. Proc. Natl. Acad. Sci. USA.]
Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms. [http://legacy.echinobase.org/Echinobase/bac_information Buckley, KM et al., 2017. Briefings in Functional Genomics].
 
<br><p>[https://wiki.echinobase.org/echinowiki/index.php/Bac_vector_library'''BAC Protocols''']</p>
<p>Screening a BAC library</p>
<p>Generating a recombinant BAC</p>
<p>BAC miniprep protocol</p>
<p>Analyzing BAC DNA by PFGE</p>
 
<br>'''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 here). Existing clones are available by request. We will also consider requests to make additional recombinant reporter constructs as time permits.
 
<p>To request a recombinant or wildtype BAC for non-commercial use:</p>
<p>1. Identify the BAC of interest computationally or by screening our libraries (available filters).</p>
<p>2. Request the BAC by emailing Veronica Hinman.</p>
 
 
'''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)

Revision as of 13:59, 29 June 2021

Table of S. purpuratus Enhancer RNAs (eRNAs)

The data are available for download here.

The Excel file is called "Table of S. purpuratus eRNAs".

The table contains eRNAs mapped to the S. purpuratus v5.0 genome.

What are eRNAs?

Enhancers are regions of DNA that are involved in regulating gene expression. Unlike promoters, these cis-regulatory elements do not have strict requirements of position or orientation. In 2010, it was discovered that enhancers can be transcribed to produce enhancer RNAs or eRNAs (reviewed by Arnold, Wells and Li, 2019). The role of eRNAs and the mechanisms involved in the regulation and expression of developmental genes is the subject of active research.