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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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AAV Purification by Iodixanol Gradient Ultracentrifugation Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.bawqifdw | This protocol goes through AAV purification by Iodixanol gradient ultracentrifugation. To see the full abstract and additional resources, visit the Addgene protocol page.Sample Data | Addgene | https://www.addgene.org/protocols/aav-purification-iodixanol-gradient-ultracentrifugation/ | 2 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. AAV Purification by Iodixanol Gradient Ultracentrifugation. protocols.io https://dx.doi.org/10.17504/protocols.io.bawqifdw | 2021-04-15 09:14:44 | |||
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General Transfection Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.bawuifew | This protocol is for general transfection. To see the full abstract and additional resources, visit the Addgene protocol page.Sample Data | Addgene | https://www.addgene.org/protocols/transfection/ | 2 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. General Transfection. protocols.io https://dx.doi.org/10.17504/protocols.io.bawuifew | 2021-04-15 09:14:35 | |||
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General Transfection Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.4xqgxmw | This protocol is for general transfection. To see the full abstract and additional resources, visit the Addgene protocol page.Sample Data | Addgene | https://www.addgene.org/protocols/transfection/ | 1 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. General Transfection. protocols.io https://dx.doi.org/10.17504/protocols.io.4xqgxmw | 2021-04-15 09:14:54 | |||
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Inoculating a Liquid Bacterial Culture Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.5abg2an | This protocol is for inoculating a liquid bacterial culture. To see the full abstract and additional resources, visit https://www.addgene.org/protocols/inoculate-bacterial-culture/. | Addgene | https://www.addgene.org/protocols/inoculate-bacterial-culture/ | 1 | 2020 | Addgene The Nonprofit Plasmid Repository 2020. Inoculating a Liquid Bacterial Culture. protocols.io https://dx.doi.org/10.17504/protocols.io.5abg2an | 2021-04-15 09:14:58 | |||
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Creating Bacterial Glycerol Stocks for Long-term Storage of Plasmids Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.4g5gty6 | This protocol is for creating bacterial glycerol stocks for long-term storage of plasmids. To see the full abstract and other resources, visit the Addgene protocol page. | Addgene | https://www.addgene.org/protocols/create-glycerol-stock/ | 1 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. Creating Bacterial Glycerol Stocks for Long-term Storage of Plasmids. protocols.io https://dx.doi.org/10.17504/protocols.io.4g5gty6 | 2021-04-15 09:15:31 | |||
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RNA Extraction Without a Kit Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.beabjaan | Coronavirus Method Development Community | This protocol describes RNA extraction without a kit. To see the full abstract and additional resources, visit https://www.addgene.org/protocols/kit-free-rna-extraction/ | Addgene | https://www.addgene.org/protocols/kit-free-rna-extraction/ | 1 | 2020 | Addgene The Nonprofit Plasmid Repository 2020. RNA Extraction Without a Kit. protocols.io https://dx.doi.org/10.17504/protocols.io.beabjaan | 2021-04-15 09:15:32 | ||
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Restriction Digest of Plasmid DNA Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.cd2s8d | Please see the Addgene website for additional details. | Addgene | http://www.addgene.org/plasmid_protocols/restriction_digest/ | 1 | 2014 | Addgene The Nonprofit Plasmid Repository 2014. Restriction Digest of Plasmid DNA. protocols.io https://dx.doi.org/10.17504/protocols.io.cd2s8d | 2021-04-15 09:15:05 | |||
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DNA Ligation Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.4g7gtzn | This protocol is for how to perform DNA ligation. To see the full abstract and other resources, visit https://www.addgene.org/protocols/dna-ligation/. | Addgene | https://www.addgene.org/protocols/dna-ligation/ | 1 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. DNA Ligation. protocols.io https://dx.doi.org/10.17504/protocols.io.4g7gtzn | 2021-04-15 09:15:16 | |||
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Pouring LB Agar Plates Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.5icg4aw | The following protocol is for making LB agar plates for the purpose of bacterial selection (500mL of LB agar makes about 25 LB agar plates). Please see the Addgene website for additional details. | Addgene | https://www.addgene.org/plasmid_protocols/bacterial_plates/ | 2 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. Pouring LB Agar Plates. protocols.io https://dx.doi.org/10.17504/protocols.io.5icg4aw | 2021-04-15 09:15:48 | |||
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AAV Titration by qPCR Using SYBR Green Technology Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.47kgzkw | This protocol goes through AAV titration by qPCR using SYBR Green Technology. To see the full abstract and additional resources, visit the Addgene protocol page.Sample DataReferencesAurnhammer C, Haase M, Muether N, Hausl M, Rauschhuber C, Huber I, Nitschko H, Busch U, Sing A, Ehrhardt A, Baiker A. Universal real-time PCR for the detection and quantification of adeno-associated virus serotype 2-derived inverted terminal repeat sequences. Hum Gene Ther Methods. 2012 Feb;23(1):18-28.PMID: 22428977 | Addgene | https://www.addgene.org/protocols/aav-titration-qpcr-using-sybr-green-technology/ | 1 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. AAV Titration by qPCR Using SYBR Green Technology. protocols.io https://dx.doi.org/10.17504/protocols.io.47kgzkw | 2021-04-15 09:15:38 | |||
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Agarose Gel Electrophoresis-Chem 584 Resource Report Resource Website |
Ken Christensen, Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.bjvnkn5e | This protocol is for agarose gel electrophoresis. To see the full abstract and additional resources, visit the Addgene protocol page. | Brigham Young University, Addgene | https://www.addgene.org/protocols/gel-electrophoresis/ | 1 | 2020 | Ken Christensen, Addgene The Nonprofit Plasmid Repository 2020. Agarose Gel Electrophoresis-Chem 584 . protocols.io https://dx.doi.org/10.17504/protocols.io.bjvnkn5e | 2021-04-15 09:15:55 | |||
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Restriction Digest of Plasmid DNA Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.63shgne | This protocol is for restriction digest of plasmid DNA. To see the full abstract and additional resources, please visit http://www.addgene.org/plasmid_protocols/restriction_digest/. | Addgene | http://www.addgene.org/plasmid_protocols/restriction_digest/ | 3 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. Restriction Digest of Plasmid DNA. protocols.io https://dx.doi.org/10.17504/protocols.io.63shgne | 2021-04-15 09:15:53 | |||
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Generating Stable Cell Lines with Lentivirus Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.4xtgxnn | This protocol is for generating stable cell lines with lentivirus. To see the full abstract and additional resources, please visit the Addgene protocol page.Sample Data | Addgene | https://www.addgene.org/protocols/generating-stable-cell-lines/ | 1 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. Generating Stable Cell Lines with Lentivirus. protocols.io https://dx.doi.org/10.17504/protocols.io.4xtgxnn | 2021-04-15 09:16:07 | |||
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Plasmid Cloning by PCR Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.43rgym6 | This protocol describes plasmid cloning by Polymerase Chain Reaction (PCR). To see the full abstract and additional resources, please visit the Addgene protocol page. | Addgene | https://www.addgene.org/protocols/pcr-cloning/ | 1 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. Plasmid Cloning by PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.43rgym6 | 2021-04-15 09:16:06 | |||
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ddPCR Titration of Lentivirus Vectors Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.be7ijhke | This protocol describes ddPCR titration of Lentivirus vectors. To see the full abstract and additional resources, visit https://www.addgene.org/protocols/lentivirus-ddpcr-titration/.This protocol was modified from the publication Wang Y, Bergelson S, Feschenko M, 2018. Sample Data: When analyzing data there should be a clear distinction between negative droplets (black) and positive droplets (blue/green).The concentration of RRE positive droplets in the untransduced control should be close to zero (A01).In this protocol, the lentiviral particles are serially diluted and used to transduce HEK293T cells. Genomic DNA is extracted from the target cells and assayed for integrated copies of RRE. Since the samples that are assayed are diluted 2-fold serially, the concentration of RRE positive droplets should decrease by a factor of 2 across the dilutions. RPP30 copies should be relatively constant across samples.In the RRE example below, 2-fold serial dilutions of a sample were loaded in wells B01-H01.As shown in the image and table below, the concentration of RRE positive droplets increases by a factor of ~2 as you progress from the higher dilutions to the lower dilutions (blue).The concentration of RPP30 positive droplets stays relatively even across samples (green).To increase the accuracy of the titer, calculate and average of several dilutions. | Addgene | https://www.addgene.org/protocols/lentivirus-ddpcr-titration/ | 1 | 2020 | Addgene The Nonprofit Plasmid Repository 2020. ddPCR Titration of Lentivirus Vectors. protocols.io https://dx.doi.org/10.17504/protocols.io.be7ijhke | 2021-04-15 09:16:03 | |||
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ddPCR titration of AAV vectors Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.bqifmubn | This protocol describes ddPCR titration of AAV vectors. To see the full abstract and additional resources, visit https://www.addgene.org/protocols/aav-ddpcr-titration/.Sample Data: When analyzing data there should be a clear distinction between negative droplets (black) and positive droplets (blue).The no template control (NTC) should be close to zero (B08). At Addgene, runs with an NTC >5 are invalid.To reduce NTC values, we recommend wiping down all pipettes and equipment with 10% bleach prior to use and keeping all reagents and samples on ice or pre-chilled 96-well freezer blocks during use.In this protocol, a dilution series is prepared for each AAV sample and the 3 final dilutions are assayed. The samples that are assayed are diluted 2-fold serially therefore, the concentration obtained by ddPCR should decrease by a factor of 2 across the dilutions. In the example below, 2-fold serial dilutions of a sample were loaded in wells A04, A05 and A06. As shown in the image and table below, the concentration of positive droplets decreases by a factor of ~2.To increase the accuracy of the titer, calculate an average of several dilutions. For additional tips on AAV titering using ddPCR, read our blog post. | Addgene | https://www.addgene.org/protocols/aav-ddpcr-titration/ | 2 | 2020 | Addgene The Nonprofit Plasmid Repository 2020. ddPCR titration of AAV vectors. protocols.io https://dx.doi.org/10.17504/protocols.io.bqifmubn | 2021-04-15 09:16:09 | |||
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AAV Production in HEK293T Cells Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.bawpifdn | This protocol is used for AAV production in HEK293T cells. To see the full abstract and additional resources, visit the Addgene protocol page.Sample Data | Addgene | https://www.addgene.org/protocols/aav-production-hek293-cells/ | 2 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. AAV Production in HEK293T Cells. protocols.io https://dx.doi.org/10.17504/protocols.io.bawpifdn | 2021-04-15 09:16:10 | |||
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Diagnostic Restriction Digest Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.4gvgtw6 | This protocol is for running a diagnostic restriction digest. To see the full abstract and other resources, visit the Addgene protocol page. | Addgene | https://www.addgene.org/protocols/diagnostic-digest/ | 1 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. Diagnostic Restriction Digest. protocols.io https://dx.doi.org/10.17504/protocols.io.4gvgtw6 | 2021-04-15 09:16:13 | |||
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Lentivirus Production Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.4xwgxpe | This protocol is for Lentivirus production. To see the full abstract and additional resources, visit the Addgene protocol page.Sample Data | Addgene | https://www.addgene.org/protocols/lentivirus-production/ | 1 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. Lentivirus Production. protocols.io https://dx.doi.org/10.17504/protocols.io.4xwgxpe | 2021-04-15 09:16:21 | |||
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Ligation Independent Cloning Resource Report Resource Website |
Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.bawjifcn | This protocol describes Ligation Independent Cloning (LIC). To see the full abstract and additional resources, please visit the Addgene protocol page. | Addgene | https://www.addgene.org/protocols/lic/ | 2 | 2019 | Addgene The Nonprofit Plasmid Repository 2019. Ligation Independent Cloning. protocols.io https://dx.doi.org/10.17504/protocols.io.bawjifcn | 2021-04-15 09:16:22 |
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