Schema for Addgene Plasmids - Addgene Plasmid Sequences alignable to the Genome
  Database: wuhCor1    Primary Table: addgene Data last updated: 2020-05-22
Big Bed File: /gbdb/wuhCor1/bbi/addgene.bb
Item Count: 24
Format description: bigbedresult gene models
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart19620Start position in chromosome
chromEnd20658End position in chromosome
name141381Name or ID of item, ideally both human readable and unique
score1000Score (0-1000)
strand++ or - for strand
addgeneLinkhttps://www.addgene.org/141381/Link to Addgene webpage for primer
definitionLentiviral_expression_of_SARS-CoV-2_protein;_transient_expression_and_generate_lentivirus.Genebank definition
keywordspLVX-EF1alpha-SARS-CoV-2-nsp15-2xStrep-IRES-PuroGenebank keywords

Sample Rows
 
chromchromStartchromEndnamescorestrandaddgeneLinkdefinitionkeywords
NC_045512v219620206581413811000+https://www.addgene.org/141381/Lentiviral_expression_of_SARS-CoV-2_protein;_transient_expression_and_generate_lentivirus.pLVX-EF1alpha-SARS-CoV-2-nsp15-2xStrep-IRES-Puro
NC_045512v221560253801413821000+https://www.addgene.org/141382/SARS-CoV-2_S_protein.pTwist-EF1alpha-SARS-CoV-2-S-2xStrep
NC_045512v221585225001450321000+https://www.addgene.org/145032/Express_SARS-CoV-2_spike_protein_with_C9_tag_at_C-terminal_in_mammalian_cells.pcDNA3.1-SARS2-Spike
NC_045512v222561231491411831000+https://www.addgene.org/141183/Mammalian_expression_plasmid_for_RBD_of_SARS-CoV-2_protein_S_fused_with_IgG1-Fc.pcDNA3-SARS-CoV-2-S-RBD-Fc
NC_045512v222561231491451451000+https://www.addgene.org/145145/Mammalian_expression_plasmid_for_RBD_of_SARS-CoV-2_protein_S_with_8his_tag.pcDNA3-SARS-CoV-2-S-RBD-8his
NC_045512v225393262011413831000+https://www.addgene.org/141383/Lentiviral_expression_of_SARS-CoV-2_protein;_transient_expression_and_generate_lentivirus.pLVX-EF1alpha-SARS-CoV-2-orf3a-2xStrep-IRES-Puro
NC_045512v225552256971413841000+https://www.addgene.org/141384/Lentiviral_expression_of_SARS-CoV-2_protein;_transient_expression_and_generate_lentivirus.pLXV-EF1alpha-2xStrep-SARS-CoV-2-orf3b-IRES-Puro
NC_045512v226521271881413861000+https://www.addgene.org/141386/Lentiviral_expression_of_SARS-CoV-2_protein;_transient_expression_and_generate_lentivirus.pLVX-EF1alpha-SARS-CoV-2-M-2xStrep-IRES-Puro
NC_045512v227202273771413871000+https://www.addgene.org/141387/Lentiviral_expression_of_SARS-CoV-2_protein;_transient_expression_and_generate_lentivirus.pLVX-EF1alpha-SARS-CoV-2-orf6-2xStrep-IRES-Puro
NC_045512v227393277521413881000+https://www.addgene.org/141388/Lentiviral_expression_of_SARS-CoV-2_protein;_transient_expression_and_generate_lentivirus.pLVX-EF1alpha-SARS-CoV-2-orf7a-2xStrep-IRES-Puro

Addgene Plasmids (addgene) Track Description
 

Description

This track shows sequences contained in plasmids that can be ordered through Addgene. Many plasmids containing SARS-CoV-2 sequences are now available and more are currently undergoing quality control analysis. Some of these plasmids are described in preprints, published articles, and summaries. For a more detailed description of some of these collections, please see the links to Addgene's webpage for each plasmid.

Some of the following plasmids are available to industry, in addition to academics and nonprofits. For more information on ordering, the link to each plasmid's homepage has been provided.

Display Conventions and Configuration

Shown on the genome are regions that can be aligned to a plasmid. The feature label is the AddGene identifier. A click on a feature shows a brief description and link to the full webpage for ordering them.

Methods

Genbank files were downloaded from Addgene and were parsed to extract relevant data fields and the plasmid nucleotide sequence. The reference sequence, SARS-CoV-2 (wuhCor1 - NC_045512v2), was then downloaded from UCSC browser and a reference database for blast alignment was created using makeblastdb. The viral region of each plasmid was then aligned using blastn. Alignments exceeding an expected value of 0.00001 were considered. The aligned sequences were then converted to bed format and the relevant Genbank data field were added. Finally, bedToBigBed was used to create the BigBed track.

Credits

Thanks to Nathan Mauldin and Jason Fernandes for making this track.

References

References can be found on the specific plasmid's webpage. Each plasmid is hosted by https://www.addgene.org.