Lexogen SENSE for de novo assembly?

Vinn · 10-16-2019, 10:01 AM

Hi folks

I wonder if anyone would like to share experience with Lexogen SENSE for de novo assembly? I am considering using the kit as it can deal with much lower RNA input (some of my samples have total RNA ca. 50 ng), but I have never tried the kit before. I am working with tree species with a genome (but not annotation) available. I am thinking about doing genome-guided de novo assembly.

Thanks in advance! Any comments and suggestions are welcome!

lexogen · 01-09-2020, 02:09 AM

Dear Vinn,
I came across your posting and hope this input helps you and others:

Lexogen's SENSE kit has been used for de novo assembly in at least these three publications:

Rizzo, Paride; Altschmied, Lothar; Stark, Pauline; Rutten, Twan; Gündel, André; Scharfenberg, Sarah et al. (2019): Discovery of key regulators of dark gland development and hypericin biosynthesis in St. John's Wort (Hypericum perforatum). In Plant Biotechnology Journal. DOI: 10.1111/pbi.13141.

Dinh Chieu, Hoang; Suwansa-Ard, Saowaros; Wang, Tianfang; Elizur, Abigail; Cummins, Scott F. (2019): Identification of neuropeptides in sea cucumber Holothuria leucospilota. In General and comparative endocrinology, p.*113229. DOI: 10.1016/j.ygcen.2019.113229.

Gault, Christine M.; Kremling, Karl A.; Buckler, Edward S. (2018): Tripsacum De novo Transcriptome Assemblies Reveal Parallel Gene Evolution with Maize after Ancient Polyploidy. In The Plant Genome 11 (3). DOI: 10.3835/plantgenome2018.02.0012.

Any further questions, comments (and of course, results!) please also direct to info@lexogen.com.

Thank you,
Lukas Paul

Sr. Mgr. Scientific Affairs
Lexogen GmbH

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
De novo genome assembly question: which assembly should I use?	tarias	Bioinformatics	1	12-07-2018 05:23 AM
Compare de-novo transcriptome assembly to genome reference guided assembly	IdoBar	Bioinformatics	1	04-04-2014 01:28 AM
Inquiry: minimum length of reads for referece-based assembly or de novo assembly	sunfuhui	Bioinformatics	1	10-04-2013 10:28 AM
Lexogen announces the "Win your SENSE Study" award	lexogen	Vendor Forum	1	04-25-2013 07:36 AM

10-16-2019, 10:01 AM	#1
Vinn Member Location: Sweden Join Date: Nov 2014 Posts: 18	Lexogen SENSE for de novo assembly? Hi folks I wonder if anyone would like to share experience with Lexogen SENSE for de novo assembly? I am considering using the kit as it can deal with much lower RNA input (some of my samples have total RNA ca. 50 ng), but I have never tried the kit before. I am working with tree species with a genome (but not annotation) available. I am thinking about doing genome-guided de novo assembly. Thanks in advance! Any comments and suggestions are welcome!

01-09-2020, 02:09 AM	#2
lexogen Registered Vendor Location: Vienna, Austria and NH, USA Join Date: Aug 2012 Posts: 49	Dear Vinn, I came across your posting and hope this input helps you and others: Lexogen's SENSE kit has been used for de novo assembly in at least these three publications: Rizzo, Paride; Altschmied, Lothar; Stark, Pauline; Rutten, Twan; Gündel, André; Scharfenberg, Sarah et al. (2019): Discovery of key regulators of dark gland development and hypericin biosynthesis in St. John's Wort (Hypericum perforatum). In Plant Biotechnology Journal. DOI: 10.1111/pbi.13141. Dinh Chieu, Hoang; Suwansa-Ard, Saowaros; Wang, Tianfang; Elizur, Abigail; Cummins, Scott F. (2019): Identification of neuropeptides in sea cucumber Holothuria leucospilota. In General and comparative endocrinology, p.*113229. DOI: 10.1016/j.ygcen.2019.113229. Gault, Christine M.; Kremling, Karl A.; Buckler, Edward S. (2018): Tripsacum De novo Transcriptome Assemblies Reveal Parallel Gene Evolution with Maize after Ancient Polyploidy. In The Plant Genome 11 (3). DOI: 10.3835/plantgenome2018.02.0012. Any further questions, comments (and of course, results!) please also direct to info@lexogen.com. Thank you, Lukas Paul Sr. Mgr. Scientific Affairs Lexogen GmbH