Davidson Lab Gene Regulatory Networks - Revision history

Ctelmer: /* Ectoderm QPCR and Nanostring Data Tables */

2023-02-15T20:49:52Z

Ectoderm QPCR and Nanostring Data Tables

← Older revision		Revision as of 20:49, 15 February 2023
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	===Ectoderm QPCR and Nanostring Data Tables===		===Ectoderm QPCR and Nanostring Data Tables===

	~~<blockquote>[[EctoQPCRandNano\|Ectoderm Network Data]]~~
	~~</blockquote>~~

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	~~'''HIGH DENSITY TIMECOURSE DATA'''~~		===High Density Timecourse Data===



	~~<div align="left">~~		-----

	~~High Density Timecourse Data [[#Top\|Back to Top]]~~

	~~</div>~~
	~~<div align="left">~~



	</div>		</div>
	<div align="left">		<div align="left">

	~~Take me directly to the~~ [~~http~~://~~legacy~~.~~echinobase~~.org/~~hd-tc~~/~~plot~~.~~cgi plotting tool~~.]		See [https://wiki.xenbase.org/echinowiki/index.php/Quantitative_Expression_Datasets_and_Plotting_Tools HERE] for these datasets and tools.

	</div>		</div>
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	<div align="left">		<div align="left">

	In order to obtain high-resolution expression profiles samples were collected at hourly intervals from fertilization to late gastrulation. Rather than rely on housekeeping genes to quantify expression level we used external standards. For this we carefully transcribed GFP RNA and RFP RNA in vitro and accurately determined its concentration. We then added a fixed number of RNA molecules to lysates of a known number of embryos. Abundance of sea urchin transcripts and standards was determined with the [http://www.nanostring.com/ NanoString nCounter], an RNA counting device, and the resulting data were converted to molecules per embryo. The measured time courses agree well with, and substantially extend, prior relative abundance measurements obtained by quantitative PCR~~. The data are available via an [http://legacy.echinobase.org/hd-tc/plot.cgi interactive plotting tool] for quick plotting of selected time courses~~. For a detailed discussion of the data please consult the paper (Materna et al., 2010).		In order to obtain high-resolution expression profiles samples were collected at hourly intervals from fertilization to late gastrulation. Rather than rely on housekeeping genes to quantify expression level we used external standards. For this we carefully transcribed GFP RNA and RFP RNA in vitro and accurately determined its concentration. We then added a fixed number of RNA molecules to lysates of a known number of embryos. Abundance of sea urchin transcripts and standards was determined with the [http://www.nanostring.com/ NanoString nCounter], an RNA counting device, and the resulting data were converted to molecules per embryo. The measured time courses agree well with, and substantially extend, prior relative abundance measurements obtained by quantitative PCR. For a detailed discussion of the data please consult the paper (Materna et al., 2010).

	</div>		</div>
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	This work is described in:<br />		This work is described in:<br />
	<br />		<br />
	Davidson et al., A Genomic Regulatory Network for Development. ''Science'' '''295''' (5560): 1669-1678, 2002. ([~~http~~://www.~~sciencemag~~.org/~~cgi~~/~~content~~/~~full/295/5560/1669~~ Available online].)<br />		Davidson et al., A Genomic Regulatory Network for Development. ''Science'' '''295''' (5560): 1669-1678, 2002. ([https://www.science.org/doi/10.1126/science.1069883 Available online].)<br />
	<br />		<br />
	Bolouri, H. and Davidson, E. H. Modeling DNA sequence-based ''cis''-regulatory gene networks. ''Dev. Biol.'' '''246''', 2-13, 2002.<br />		Bolouri, H. and Davidson, E. H. Modeling DNA sequence-based ''cis''-regulatory gene networks. ''Dev. Biol.'' '''246''', 2-13, 2002.<br />
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	Li, E. and Davidson, E. H. Building developmental gene regulatory networks. ''Birth Defects Res. (Part C)'' '''87''', 123-130, 2009.<br />		Li, E. and Davidson, E. H. Building developmental gene regulatory networks. ''Birth Defects Res. (Part C)'' '''87''', 123-130, 2009.<br />
	<br />		<br />
	Bolouri, H. and Davidson, E. H. The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example. ''Dev. Biol.''~~, in press~~, available [~~http~~://dx.~~doi~~.~~org~~/~~10.1016~~/~~j.ydbio.2009.06.007~~ online].<br />		Bolouri, H. and Davidson, E. H. The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example. ''Dev. Biol.'', available [https://www.sciencedirect.com/science/article/pii/S001216060900918X?via%3Dihub online].<br />
	<br />		<br />
	Ben-Tabou de-Leon, S. and Davidson, E. H. Experimentally based sea urchin gene regulatory network and the causal explanation of developmental phenomenology. ''Wiley Interdisciplinary Reviews: Systems Biol. & Med.'' '''1''', 237-246, 2009.<br />		Ben-Tabou de-Leon, S. and Davidson, E. H. Experimentally based sea urchin gene regulatory network and the causal explanation of developmental phenomenology. ''Wiley Interdisciplinary Reviews: Systems Biol. & Med.'' '''1''', 237-246, 2009.<br />
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	Smith, J. and Davidson, E. H. Regulative recovery in the sea urchin embryo, and the stabilizing role of fail-safe gene network wiring. ''Proc. Natl, Acad. Sci. USA'', '''106''', 18291-18296, 2009.<br />		Smith, J. and Davidson, E. H. Regulative recovery in the sea urchin embryo, and the stabilizing role of fail-safe gene network wiring. ''Proc. Natl, Acad. Sci. USA'', '''106''', 18291-18296, 2009.<br />
	<br />		<br />
	Davidson, E. H. Network design principles from the sea urchin embryo. ''Curr Opin. in Genetics Dev.''~~, in press~~, available [~~http~~://dx.~~doi~~.~~org~~/~~10.1016~~/~~j.gde.2009.10.007~~ online].<br />		Davidson, E. H. Network design principles from the sea urchin embryo. ''Curr Opin. in Genetics Dev.'', available [https://www.sciencedirect.com/science/article/abs/pii/S0959437X09001555?via%3Dihub online].<br />
	<br />		<br />
	Davidson, E. H. and Erwin, D. H. Evolutionary innovation and stability in animal gene networks. ''J. Evol. Zool.'', in press.<br />		Davidson, E. H. and Erwin, D. H. Evolutionary innovation and stability in animal gene networks. ''J. Evol. Zool.'', in press.<br />
	<br />		<br />
	Cameron, R. A. and Davidson, E. H. Flexibility of transcription factor target site position in conserved cis-regulatory modules. ''Dev. Biol.'', in press, available [~~http~~://dx.~~doi~~.~~org~~/~~10.1016~~/~~j.ydbio.2009.09.018~~ online].<br />		Cameron, R. A. and Davidson, E. H. Flexibility of transcription factor target site position in conserved cis-regulatory modules. ''Dev. Biol.'', in press, available [https://www.sciencedirect.com/science/article/pii/S0012160609012032?via%3Dihub online].<br />
	<br />		<br />
	Peter, I. S. and Davidson, E. H. The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage. ''Dev. Biol.''~~, in press~~, available [~~http~~://dx.~~doi~~.~~org~~/~~10.1016~~/~~j.ydbio.2009.10.037~~ online].<br />		Peter, I. S. and Davidson, E. H. The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage. ''Dev. Biol.'', available [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981691/ online].<br />
	<br />		<br />
	Peter, I. S. and Davidson, E. H. Modularity and design principles in the sea urchin embryo gene regulatory network. ''FEBS Letters'', ~~in press~~.<br />		Peter, I. S. and Davidson, E. H. Modularity and design principles in the sea urchin embryo gene regulatory network. ''FEBS Letters'', available [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2810318/ online].<br />
	<br />		<br />

Ctelmer: /* BioTapestry Interactive Network Viewer for Ectoderm */

2023-02-15T20:33:57Z

BioTapestry Interactive Network Viewer for Ectoderm

← Older revision		Revision as of 20:33, 15 February 2023
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	===BioTapestry Interactive Network Viewer for Ectoderm ===		===BioTapestry Interactive Network Viewer for Ectoderm ===

	<blockquote>The ectoderm network model can be viewed ~~using the [~~http://www.biotapestry.org/ '''~~BioTapestry Interactive Network Viewer''']~~, which is now a web application that runs in all modern browsers. For more information about BioTapestry and running it~~, since the above sections [[#BioTapestryAbout\|About The BioTapestry Editor]] and [[#QuickStart\|BioTapestry Viewer "~~Quick Start~~" User~~'~~s Guide]].~~		<blockquote>The ectoderm network model can be viewed at '''<nowiki>http://www.biotapestry.org/#currentDeploy</nowiki>''', which is now a web application that runs in all modern browsers. For more information about BioTapestry and running it a Quick Start Tutorial is at '''<nowiki>http://www.biotapestry.org/quickStart/QuickStart.html</nowiki>'''.

	[http://~~grns~~.biotapestry.org/~~SpEcto~~/ ~~Click Here to View the Ectoderm Model Using the BioTapestry Interactive Network Viewer]~~
	</blockquote>		</blockquote>
	<div>		<div>

Ctelmer: /* About The BioTapestry Editor */

2023-02-15T20:28:18Z

About The BioTapestry Editor

← Older revision		Revision as of 20:28, 15 February 2023
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	== About The BioTapestry Editor ==		== About The BioTapestry Editor ==

	<blockquote>BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks. The network '''viewer''' used here is a simplified, browser-based version of the full-featured network '''editor'''~~, which is available from [http://www.biotapestry.org BioTapestry.org]~~.		<blockquote>BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks. The network '''viewer''' used here is a simplified, browser-based version of the full-featured network '''editor'''.

	* With the current version of BioTapestry, the user can: 1) draw networks by hand, or 2) specify a list of interactions either in interactive tables or comma-separated value (CSV) input files and then have the network laid out automatically. Also, when provided with separate tables of experimental data, BioTapestry can automatically show hourly changes in the network state.		* With the current version of BioTapestry, the user can: 1) draw networks by hand, or 2) specify a list of interactions either in interactive tables or comma-separated value (CSV) input files and then have the network laid out automatically. Also, when provided with separate tables of experimental data, BioTapestry can automatically show hourly changes in the network state.
	* BioTapestry development is ongoing, with continuing new releases that improve the functionality and ease-of-use of the software. More information on plans for future development are available on the [http://www.biotapestry.org BioTapestry home page].
	</blockquote>		</blockquote>

	== BioTapestry Viewer "Quick Start" User's Guide ==		== BioTapestry Viewer "Quick Start" User's Guide ==
	===Levels of Network Models===		===Levels of Network Models===

Ctelmer: /* BioTapestry Interactive Network Viewer */

2023-02-15T20:27:14Z

BioTapestry Interactive Network Viewer

← Older revision		Revision as of 20:27, 15 February 2023
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	<blockquote>The endomesoderm network model can be viewed ~~using the [~~http://www.biotapestry.org/ '''~~BioTapestry Interactive Network Viewer''']~~, which is now a web application that runs in all modern browsers. BioTapestry was originally developed by William Longabaugh, Eric Davidson, and Hamid Bolouri, supported by a grant by NIH General Medical. Active development is continuing with support from NIH Child Health and Human Development. The most recent release is ~~[http://www.biotapestry.org/#whatsNew~~ Version 7] (September 2014), which supports both the ~~new~~ web browser-based Viewer, and the traditional Java Editor. The static-image version and Java WebStart Viewer version of the endomesoderm network have been discontinued.		<blockquote>The endomesoderm network model can be viewed at '''<nowiki>http://www.biotapestry.org/</nowiki>''', which is now a web application that runs in all modern browsers. BioTapestry was originally developed by William Longabaugh, Eric Davidson, and Hamid Bolouri, supported by a grant by NIH General Medical. Active development is continuing with support from NIH Child Health and Human Development. The most recent release is Version 7 (September 2014), which supports both the web browser-based Viewer, and the traditional Java Editor. The static-image version and Java WebStart Viewer version of the endomesoderm network have been discontinued.

			The Online GRN Repository can be found at '''<nowiki>http://www.biotapestry.org/#grns</nowiki>'''.

	~~[http://grns.biotapestry.org/SpEndomes/ Click Here to View the Endomesoderm Model Using the BioTapestry Interactive Network Viewer]~~
	~~</blockquote>~~

	== About The BioTapestry Editor ==		== About The BioTapestry Editor ==

imported>Ctelmer: /* Endomesoderm Specification 21 to 30 Hours: View From All Nuclei */

2020-07-16T18:46:28Z

Endomesoderm Specification 21 to 30 Hours: View From All Nuclei

← Older revision		Revision as of 18:46, 16 July 2020
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	</blockquote>		</blockquote>
	The architecture of the network is based on perturbation and expression data, on data from ''cis''-regulatory analyses for several genes, and on other experiments discussed in text. See the endomesoderm network perturbation QPCR data for quantitative results of perturbation experiments and temporal details. Each short horizontal line from which a bent arrow extends to indicate transcription represents the ''cis''-regulatory element that is responsible for expression of the gene named in the domain shown. Embryonic gene expression was perturbed in specific ways by use of antisense morpholino-substituted oligonucleotides by introduction of mRNA encoding Engrailed repressor domain fusions or mRNA encoding the normal protein product of the gene; by introduction of genetic expression constructs; by interference with the β-catenin/Tcf signal transduction system using overexpression of mRNA encoding an intracellular domain of cadherin; or by interference with the Notch (N) signaling system by overexpression of mRNA encoding the extracellular domain of the N receptor. RNA was extracted from embryos grown from eggs injected with the respective perturbation reagents and converted to cDNA. This was utilized in multiplexed quantitative PCR (QPCR) experiments to assess effects of each perturbation on the other genes indicated in the Figure. The arrows and barred lines indicate the normal function of the gene (activation or repression) as deduced from changes in transcript levels due to the perturbations. Minimum significance levels for inclusion in the model are three-fold increases or decreases in amount of transcript as a result of the perturbation; effects range up to several hundred fold. The relationships shown may in some cases be indirect, though all known or suspected indirect relationships have been excluded from the model. For linkages that are direct each input arrow constitutes a prediction of specific transcription factor target site sequence(s) in the relevant ''cis''-regulatory control element. Experimental ''cis''-regulatory results provide additional direct evidence; green diamonds indicate reported experimental evidence validates expected target site. Many genes are initially expressed over broader ranges, and their expression later resolves to the definitive domains indicated by their backgrounds. The rectangles in the lower tier of the diagram (with the exception of Small Mic/CP) show downstream differentiation genes. Dashed lines indicate inferred or possibly indirect relationships. Arrows inserted in arrow tails indicate intercellular signaling interactions. Large open ovals represent cytoplasmic biochemical interactions at the protein level, e.g., those responsible for nuclearization of β-catenin, the effect of Delta on Notch (Jacobsen et al., 1998) or of Neuralized on Delta (Yeh et al., 2000, 2001). Much data from experimental embryology and molecular biology are included in this model; for references see Davidson et al., ''Dev. Biol.'' '''246''', 162-190, 2002.		The architecture of the network is based on perturbation and expression data, on data from ''cis''-regulatory analyses for several genes, and on other experiments discussed in text. See the [https://wiki.echinobase.org/echinowiki/index.php/Endomes_QPCR endomesoderm network perturbation QPCR data] for quantitative results of perturbation experiments and temporal details. Each short horizontal line from which a bent arrow extends to indicate transcription represents the ''cis''-regulatory element that is responsible for expression of the gene named in the domain shown. Embryonic gene expression was perturbed in specific ways by use of antisense morpholino-substituted oligonucleotides by introduction of mRNA encoding Engrailed repressor domain fusions or mRNA encoding the normal protein product of the gene; by introduction of genetic expression constructs; by interference with the β-catenin/Tcf signal transduction system using overexpression of mRNA encoding an intracellular domain of cadherin; or by interference with the Notch (N) signaling system by overexpression of mRNA encoding the extracellular domain of the N receptor. RNA was extracted from embryos grown from eggs injected with the respective perturbation reagents and converted to cDNA. This was utilized in multiplexed quantitative PCR (QPCR) experiments to assess effects of each perturbation on the other genes indicated in the Figure. The arrows and barred lines indicate the normal function of the gene (activation or repression) as deduced from changes in transcript levels due to the perturbations. Minimum significance levels for inclusion in the model are three-fold increases or decreases in amount of transcript as a result of the perturbation; effects range up to several hundred fold. The relationships shown may in some cases be indirect, though all known or suspected indirect relationships have been excluded from the model. For linkages that are direct each input arrow constitutes a prediction of specific transcription factor target site sequence(s) in the relevant ''cis''-regulatory control element. Experimental ''cis''-regulatory results provide additional direct evidence; green diamonds indicate reported experimental evidence validates expected target site. Many genes are initially expressed over broader ranges, and their expression later resolves to the definitive domains indicated by their backgrounds. The rectangles in the lower tier of the diagram (with the exception of Small Mic/CP) show downstream differentiation genes. Dashed lines indicate inferred or possibly indirect relationships. Arrows inserted in arrow tails indicate intercellular signaling interactions. Large open ovals represent cytoplasmic biochemical interactions at the protein level, e.g., those responsible for nuclearization of β-catenin, the effect of Delta on Notch (Jacobsen et al., 1998) or of Neuralized on Delta (Yeh et al., 2000, 2001). Much data from experimental embryology and molecular biology are included in this model; for references see Davidson et al., ''Dev. Biol.'' '''246''', 162-190, 2002.

imported>Ctelmer: /* Endomesoderm Specification 21 to 30 Hours: View From All Nuclei */

2020-07-16T18:40:08Z

Endomesoderm Specification 21 to 30 Hours: View From All Nuclei

← Older revision		Revision as of 18:40, 16 July 2020
Line 148:		Line 148:

	</blockquote>		</blockquote>
	The architecture of the network is based on perturbation and expression data, on data from ''cis''-regulatory analyses for several genes, and on other experiments discussed in text. See the ~~[[qpcr.html\|~~endomesoderm network perturbation QPCR data]] for quantitative results of perturbation experiments and temporal details. Each short horizontal line from which a bent arrow extends to indicate transcription represents the ''cis''-regulatory element that is responsible for expression of the gene named in the domain shown. Embryonic gene expression was perturbed in specific ways by use of antisense morpholino-substituted oligonucleotides by introduction of mRNA encoding Engrailed repressor domain fusions or mRNA encoding the normal protein product of the gene; by introduction of genetic expression constructs; by interference with the β-catenin/Tcf signal transduction system using overexpression of mRNA encoding an intracellular domain of cadherin; or by interference with the Notch (N) signaling system by overexpression of mRNA encoding the extracellular domain of the N receptor. RNA was extracted from embryos grown from eggs injected with the respective perturbation reagents and converted to cDNA. This was utilized in multiplexed quantitative PCR (QPCR) experiments to assess effects of each perturbation on the other genes indicated in the Figure. The arrows and barred lines indicate the normal function of the gene (activation or repression) as deduced from changes in transcript levels due to the perturbations. Minimum significance levels for inclusion in the model are three-fold increases or decreases in amount of transcript as a result of the perturbation; effects range up to several hundred fold. The relationships shown may in some cases be indirect, though all known or suspected indirect relationships have been excluded from the model. For linkages that are direct each input arrow constitutes a prediction of specific transcription factor target site sequence(s) in the relevant ''cis''-regulatory control element. Experimental ''cis''-regulatory results provide additional direct evidence; green diamonds indicate reported experimental evidence validates expected target site. Many genes are initially expressed over broader ranges, and their expression later resolves to the definitive domains indicated by their backgrounds. The rectangles in the lower tier of the diagram (with the exception of Small Mic/CP) show downstream differentiation genes. Dashed lines indicate inferred or possibly indirect relationships. Arrows inserted in arrow tails indicate intercellular signaling interactions. Large open ovals represent cytoplasmic biochemical interactions at the protein level, e.g., those responsible for nuclearization of β-catenin, the effect of Delta on Notch (Jacobsen et al., 1998) or of Neuralized on Delta (Yeh et al., 2000, 2001). Much data from experimental embryology and molecular biology are included in this model; for references see Davidson et al., ''Dev. Biol.'' '''246''', 162-190, 2002.		The architecture of the network is based on perturbation and expression data, on data from ''cis''-regulatory analyses for several genes, and on other experiments discussed in text. See the endomesoderm network perturbation QPCR data for quantitative results of perturbation experiments and temporal details. Each short horizontal line from which a bent arrow extends to indicate transcription represents the ''cis''-regulatory element that is responsible for expression of the gene named in the domain shown. Embryonic gene expression was perturbed in specific ways by use of antisense morpholino-substituted oligonucleotides by introduction of mRNA encoding Engrailed repressor domain fusions or mRNA encoding the normal protein product of the gene; by introduction of genetic expression constructs; by interference with the β-catenin/Tcf signal transduction system using overexpression of mRNA encoding an intracellular domain of cadherin; or by interference with the Notch (N) signaling system by overexpression of mRNA encoding the extracellular domain of the N receptor. RNA was extracted from embryos grown from eggs injected with the respective perturbation reagents and converted to cDNA. This was utilized in multiplexed quantitative PCR (QPCR) experiments to assess effects of each perturbation on the other genes indicated in the Figure. The arrows and barred lines indicate the normal function of the gene (activation or repression) as deduced from changes in transcript levels due to the perturbations. Minimum significance levels for inclusion in the model are three-fold increases or decreases in amount of transcript as a result of the perturbation; effects range up to several hundred fold. The relationships shown may in some cases be indirect, though all known or suspected indirect relationships have been excluded from the model. For linkages that are direct each input arrow constitutes a prediction of specific transcription factor target site sequence(s) in the relevant ''cis''-regulatory control element. Experimental ''cis''-regulatory results provide additional direct evidence; green diamonds indicate reported experimental evidence validates expected target site. Many genes are initially expressed over broader ranges, and their expression later resolves to the definitive domains indicated by their backgrounds. The rectangles in the lower tier of the diagram (with the exception of Small Mic/CP) show downstream differentiation genes. Dashed lines indicate inferred or possibly indirect relationships. Arrows inserted in arrow tails indicate intercellular signaling interactions. Large open ovals represent cytoplasmic biochemical interactions at the protein level, e.g., those responsible for nuclearization of β-catenin, the effect of Delta on Notch (Jacobsen et al., 1998) or of Neuralized on Delta (Yeh et al., 2000, 2001). Much data from experimental embryology and molecular biology are included in this model; for references see Davidson et al., ''Dev. Biol.'' '''246''', 162-190, 2002.


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	<div style="clear: both;"></div>		<div style="clear: both;"></div>

	===PMC Specification 6 to 30 Hours: View From All Nuclei===		===PMC Specification 6 to 30 Hours: View From All Nuclei===

imported>Ctelmer: /* ENDOMESODERM GENE NETWORK */

2020-07-16T16:25:17Z

ENDOMESODERM GENE NETWORK

← Older revision		Revision as of 16:25, 16 July 2020
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	=ENDOMESODERM GENE NETWORK=		=ENDOMESODERM GENE NETWORK=

			Please note that the last coding update to the BioTapestry version of the Sea Urchin GRN was 2019 and the last GRN update was 2014.

	== BioTapestry Interactive Network Viewer ==		== BioTapestry Interactive Network Viewer ==

imported>Ctelmer: /* Ectoderm QPCR and Nanostring Data Tables */

2020-07-16T16:14:48Z

Ectoderm QPCR and Nanostring Data Tables

← Older revision		Revision as of 16:14, 16 July 2020
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	<div align="left">		<div align="left">

	Take me directly to the [http://echinobase.org/hd-tc/plot.cgi plotting tool.]		Take me directly to the [http://legacy.echinobase.org/hd-tc/plot.cgi plotting tool.]

	</div>		</div>
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	<div align="left">		<div align="left">

	In order to obtain high-resolution expression profiles samples were collected at hourly intervals from fertilization to late gastrulation. Rather than rely on housekeeping genes to quantify expression level we used external standards. For this we carefully transcribed GFP RNA and RFP RNA in vitro and accurately determined its concentration. We then added a fixed number of RNA molecules to lysates of a known number of embryos. Abundance of sea urchin transcripts and standards was determined with the [http://www.nanostring.com/ NanoString nCounter], an RNA counting device, and the resulting data were converted to molecules per embryo. The measured time courses agree well with, and substantially extend, prior relative abundance measurements obtained by quantitative PCR. The data are available via an [http://echinobase.org/hd-tc/plot.cgi interactive plotting tool] for quick plotting of selected time courses. For a detailed discussion of the data please consult the paper (Materna et al., 2010).		In order to obtain high-resolution expression profiles samples were collected at hourly intervals from fertilization to late gastrulation. Rather than rely on housekeeping genes to quantify expression level we used external standards. For this we carefully transcribed GFP RNA and RFP RNA in vitro and accurately determined its concentration. We then added a fixed number of RNA molecules to lysates of a known number of embryos. Abundance of sea urchin transcripts and standards was determined with the [http://www.nanostring.com/ NanoString nCounter], an RNA counting device, and the resulting data were converted to molecules per embryo. The measured time courses agree well with, and substantially extend, prior relative abundance measurements obtained by quantitative PCR. The data are available via an [http://legacy.echinobase.org/hd-tc/plot.cgi interactive plotting tool] for quick plotting of selected time courses. For a detailed discussion of the data please consult the paper (Materna et al., 2010).

	</div>		</div>

imported>BArsh: /* Ectoderm QPCR and Nanostring Data Tables */

2020-03-27T02:03:18Z

Ectoderm QPCR and Nanostring Data Tables

← Older revision		Revision as of 02:03, 27 March 2020
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	===Ectoderm QPCR and Nanostring Data Tables===		===Ectoderm QPCR and Nanostring Data Tables===

	<blockquote>[[~~ectoQPCRandNano.html~~\|Ectoderm Network Data]]		<blockquote>[[EctoQPCRandNano\|Ectoderm Network Data]]
	</blockquote>		</blockquote>

imported>BArsh at 01:29, 27 March 2020

2020-03-27T01:29:29Z

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 =ENDOMESODERM GENE NETWORK=
 == BioTapestry Interactive Network Viewer ==
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 </div></blockquote>
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