Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Adaptor Ligation Mixture (E7370) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cg6tzd | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/2012/11/15/adaptor-ligation-e7370 | 1 | 2015 | New England Biolabs 2015. Adaptor Ligation Mixture (E7370). protocols.io dx.doi.org/10.17504/protocols.io.cg6tzd | 2021-03-29 03:08:01 | |||
|
PCR Using Q5U Hot Start High-Fidelity DNA Polymerase (NEB #M0515): Amplification of bisulfite-converted, deaminated, or damaged DNA (Including FFPE DNA) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.7sdhna6 | New England Biolabs (NEB) | Q5U Hot Start High-Fidelity DNA Polymerase is a modified version of Q5®High-Fidelity DNA Polymerase, a novel thermostable DNA polymerase that possesses 3′ to 5′ exonuclease activity, and is fused to a processivity-enhancing Sso7d domain. Q5U contains a mutation in the uracil-binding pocket that enables the ability to read and amplify templates containing uracil and inosine bases. | New England Biolabs | https://www.neb.com/protocols/2019/07/02/pcr-using-q5u-hot-start-high-fidelity-dna-polymerase-neb-m0515 | 1 | 2020 | New England Biolabs 2020. PCR Using Q5U Hot Start High-Fidelity DNA Polymerase (NEB #M0515): Amplification of bisulfite-converted, deaminated, or damaged DNA (Including FFPE DNA). protocols.io dx.doi.org/10.17504/protocols.io.7sdhna6 | 2021-03-29 03:08:09 | ||
|
A-Tailing with Taq Polymerase Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.crvv65 | New England Biolabs (NEB) | This protocol can be used to add As to the blunt-ends of DNA fragments that have been amplified using a high-fidelity polymerase (such as Q5® High Fidelity DNA Polymerase). | New England Biolabs | https://www.neb.com/protocols/2013/11/01/a-tailing-with-taq-polymerase | 1 | 2015 | New England Biolabs 2015. A-Tailing with Taq Polymerase. protocols.io dx.doi.org/10.17504/protocols.io.crvv65 | 2021-03-29 03:11:21 | ||
|
Mixture for M0267 Taq with ThermoPol Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cigubv | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/1/01/01/taq-dna-polymerase-with-thermopol-buffer-m0267 | 1 | 2015 | New England Biolabs 2015. Mixture for M0267 Taq with ThermoPol. protocols.io dx.doi.org/10.17504/protocols.io.cigubv | 2021-03-29 03:11:29 | |||
|
Protocol for removing ssDNA from dsDNA or RNA Samples (NEB #M0568) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.7ryhm7w | New England Biolabs (NEB) | The protocol described below will enable degradation of up to 20 pmol of a 25 nt ssDNA (~ 200 ng). In order to degrade larger amounts of ssDNA or ssDNAs longer than 25 nt, we recommend adding more enzyme instead of extending the reaction time. Users should note that ssDNAs longer than 25 nt may form secondary structures that hinder Thermolabile Exonuclease I activity. | New England Biolabs | https://neb.com/protocols/2018/08/06/protocol-for-removing-ssdna-from-dsdna-or-rna-samples-m0568 | 1 | 2020 | New England Biolabs 2020. Protocol for removing ssDNA from dsDNA or RNA Samples (NEB #M0568). protocols.io dx.doi.org/10.17504/protocols.io.7ryhm7w | 2021-03-29 03:11:40 | ||
|
M0368 RNA and Primer mixture Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.chut6v | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/2012/10/03/first-strand-cdna-synthesis-kit-using-protoscript-ii-reverse-transcriptase-m0368 | 1 | 2014 | New England Biolabs 2014. M0368 RNA and Primer mixture. protocols.io dx.doi.org/10.17504/protocols.io.chut6v | 2021-03-29 03:11:50 | |||
|
M0348 Digestion Mixture Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cr5v85 | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/1/01/01/digestion-with-nebnext-dsdna-fragmentase-m0348 | 1 | 2015 | New England Biolabs 2015. M0348 Digestion Mixture. protocols.io dx.doi.org/10.17504/protocols.io.cr5v85 | 2021-03-29 03:08:43 | |||
|
Mixture for M0492 Q5 2X Master Mix Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cijucm | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/2012/08/29/protocol-for-q5-high-fidelity-2x-master-mix-m0492 | 1 | 2014 | New England Biolabs 2014. Mixture for M0492 Q5 2X Master Mix. protocols.io dx.doi.org/10.17504/protocols.io.cijucm | 2021-03-29 03:08:44 | |||
|
Protein Expression Using BL21(DE3), Large Scale (C2527) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cjrum5 | New England Biolabs (NEB) | This is the protocol for a large-scale Protein Expression Using BL21(DE3) Competent E. coli cells(C2527). | New England Biolabs | https://www.neb.com/protocols/1/01/01/protein-expression-using-bl21de3-c2527 | 1 | 2014 | New England Biolabs 2014. Protein Expression Using BL21(DE3), Large Scale (C2527). protocols.io dx.doi.org/10.17504/protocols.io.cjrum5 | 2021-03-29 03:08:51 | ||
|
M0368 RT Mixture Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.chwt7d | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/2012/10/03/first-strand-cdna-synthesis-kit-using-protoscript-ii-reverse-transcriptase-m0368 | 1 | 2014 | New England Biolabs 2014. M0368 RT Mixture. protocols.io dx.doi.org/10.17504/protocols.io.chwt7d | 2021-03-29 03:08:51 | |||
|
Blunting Protocol for NEB PCR Cloning Kit (E1202) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.crpv5m | New England Biolabs (NEB) | This is the blunting protocol for NEB PCR Cloning Kit (E1202) | New England Biolabs | https://www.neb.com/protocols/1/01/01/blunting-protocol-e1202 | 1 | 2015 | New England Biolabs 2015. Blunting Protocol for NEB PCR Cloning Kit (E1202). protocols.io dx.doi.org/10.17504/protocols.io.crpv5m | 2021-03-29 03:09:20 | ||
|
Protocol for Use with Standard Insert Libraries (370-420 bp) (NEB#E7120) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.bfuejnte | New England Biolabs (NEB) | This protocol details how to construct DNA libraries from start to finish using NEBNext reagents.The corresponding NEB manual is here: https://www.neb.com/-/media/nebus/files/manuals/manuale7120.pdf and this protocol relates to section 1.OverviewThe Enzymatic Methyl-seq kit (EM-seq) for Illumina contains all the components needed to make libraries that are enzymatically modified to detect 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC). Figure 1 is an overview of the EM-seq workflow. Firstly, a library is made by ligating EM-seq adaptor to sheared end repaired/dA-tailed genomic DNA. This is followed by two sets of enzymatic conversion steps to differentiate cytosines from 5mC and 5hmC. Finally, libraries are PCR amplified before sequencing.Figure 2 shows a comparison of the sodium bisulfite and EM-seq methods. Sodium bisulfite treatment of DNA results in the deamination of cytosines into uracils, however the modified forms of cytosine (5mC and 5hmC) are not deaminated. Therefore, the preference of bisulfite to chemically deaminate cytosines enables the methylation status of cytosines to be determined. When bisulfite treated DNA is PCR amplified, uracils are replaced by thymines and the 5mC/5hmC are replaced by cytosines. Once sequenced, unmethylated cytosines are represented by thymines and 5mC and 5hmC are represented by cytosines. By comparing sequences to non-converted genomes the appropriate methylation status can be assessed.Enzymatic Methyl-seq is a two step enzymatic conversion process to detect modified cytosines. The first step uses TET2 and an oxidation enhancer to protect modified cytosines from downstream deamination. TET2 enzymatically oxidizes 5mC and 5hmC through a cascade reaction into 5-carboxycytosine [5-methylcytosine (5mC) Þ5-hydroxymethylcytosine (5hmC) Þ 5-formylcytosine (5fC) Þ 5- carboxycytosine (5caC)]. This protects 5mC and 5hmC from deamination. 5hmC can also be protected from deamination by glucosylation to form 5ghmc using the oxidation enhancer. The second enzymatic step uses APOBEC to deaminate C but does not convert 5caC and 5ghmC. The resulting converted sequence can be analyzed like bisulfite-treated DNA. Typical aligners used to analyze data include but are not limited to Bismark and BWAMeth.The workflow described in the NEBNext Enzymatic Methyl-seq Kit is user-friendly and enables methylation detection from inputs ranging between 10 ng–200 ng. EM-seq converted DNA is more intact than bisulfite-converted DNA, resulting in libraries with longer sequencing reads, reduced GC bias and more even genome coverage. Each kit component must pass rigorous quality control standards, and for each new lot the entire set of reagents is functionally validated together by construction of indexed libraries and sequenced on an Illumina sequencing platform. For larger volume requirements, customized and bulk packaging is available by purchasing through the Custom Solutions department at NEB. Please contact [email protected] for further information. | New England Biolabs | https://www.neb.com/protocols/2019/03/28/protocol-for-use-with-standard-insert-libraries-370-420-bp-e7120 | 1 | 2020 | New England Biolabs 2020. Protocol for Use with Standard Insert Libraries (370-420 bp) (NEB#E7120). protocols.io dx.doi.org/10.17504/protocols.io.bfuejnte | 2021-03-29 03:09:27 | ||
|
Quick Protocol for Monarch® PCR & DNA Cleanup Kit (5 ?g) (NEB #T1030) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.ejxbcpn | New England Biolabs (NEB) | This is the "quick" version of Monarch® PCR & DNA Cleanup Kit (5 μg) Protocol (NEB #T1030). For the full protocol, please click here. | New England Biolabs | https://www.neb.com/protocols/2015/12/08/quick-protocol-for-monarch-pcr-dna-cleanup-kit-5-g-t1030 | 1 | 2016 | New England Biolabs 2016. Quick Protocol for Monarch® PCR & DNA Cleanup Kit (5 ?g) (NEB #T1030). protocols.io dx.doi.org/10.17504/protocols.io.ejxbcpn | 2021-03-29 03:07:34 | ||
|
NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®) (NEB #E7650S/L) Resource Report Resource Website |
Isabel Gautreau | 10.17504/protocols.io.bsy4nfyw | New England Biolabs (NEB), Coronavirus Method Development Community | This protocol is about the NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®). | New England Biolabs | https://www.neb.com/-/media/nebus/files/manuals/manuale7650.pdf?rev=f37be6e42b4f486f888f204b83907d3f&hash=69F40067B46B925A7D45F5A6D418095F | 2 | 2021 | Isabel Gautreau 2021. NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®) (NEB #E7650S/L). protocols.io dx.doi.org/10.17504/protocols.io.bsy4nfyw | 2021-03-29 03:10:36 | ||
|
T4 DNA Ligase Reaction Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.irwcd7e | New England Biolabs (NEB) | This is the reaction for the "Ligation Protocol with T4 DNA Ligase" | New England Biolabs | https://www.neb.com/protocols/1/01/01/dna-ligation-with-t4-dna-ligase-m0202 | 2 | 2017 | New England Biolabs 2017. T4 DNA Ligase Reaction. protocols.io dx.doi.org/10.17504/protocols.io.irwcd7e | 2021-03-29 03:10:42 | ||
|
Single-temp DD Reaction Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cjjukm | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/2014/05/07/double-digest-protocol-with-standard-restriction-enzymes | 1 | 2014 | New England Biolabs 2014. Single-temp DD Reaction. protocols.io dx.doi.org/10.17504/protocols.io.cjjukm | 2021-03-29 03:10:42 | |||
|
Protocol for Exo-CIP™ Rapid PCR Cleanup (#E1050) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.8yahxse | New England Biolabs (NEB) | Exo-CIP™ Rapid PCR Cleanup KitRapidly degrade residual PCR primers and dephosphorylate excess dNTPs after amplificationReaction complete in 4 minutesThermolabile formulation can be heat inactivated in 1 minute at 80°CPCR product can be used directly in downstream applicationsCompatible with commonly-used reaction buffers | New England Biolabs | https://neb.com/protocols/2019/01/16/protocol-for-exo-ciprapid-pcr-cleanup-e1050 | 1 | 2020 | New England Biolabs 2020. Protocol for Exo-CIP™ Rapid PCR Cleanup (#E1050). protocols.io dx.doi.org/10.17504/protocols.io.8yahxse | 2021-03-29 03:10:42 | ||
|
Electroporation Protocol Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cruv6v | New England Biolabs (NEB) | This protocol may be used with electrocompetent cells prepared by you according to this protocol. | New England Biolabs | https://www.neb.com/protocols/2012/06/21/making-your-own-electrocompetent-cells | 1 | 2015 | New England Biolabs 2015. Electroporation Protocol. protocols.io dx.doi.org/10.17504/protocols.io.cruv6v | 2021-03-29 03:10:52 | ||
|
Mixture for M0530 Phusion PCR Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cgztx5 | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/1/01/01/pcr-protocol-m0530 | 1 | 2015 | New England Biolabs 2015. Mixture for M0530 Phusion PCR. protocols.io dx.doi.org/10.17504/protocols.io.cgztx5 | 2021-03-29 03:10:54 | |||
|
Suggested protocol for loading a DNA Ladder/marker Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cq4vyv | New England Biolabs (NEB) | This is the suggested protocol for use with λ DNA-Mono Cut Mix (N3019), фX174 DNA-HaeIII Digest (N3026),pBR322 DNA-BstNI Digest (N3031), pBR322 DNA-MspI Digest (N3032), 2-Log DNA Ladder (0.1-10.0 kb) (N3200), 100 bp DNA Ladder (N3231), 1 kb DNA Ladder (N3232), Low Molecular Weight DNA Ladder (N3233), and 50 bp DNA Ladder (N3236) | New England Biolabs | https://www.neb.com/protocols/1/01/01/suggested-protocol-for-loading-a-dna-ladder-marker | 1 | 2015 | New England Biolabs 2015. Suggested protocol for loading a DNA Ladder/marker. protocols.io dx.doi.org/10.17504/protocols.io.cq4vyv | 2021-03-29 03:10:54 |
Can't find your Protocol?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. If you want to find a specific protocol and you know the DOI of the protocol already, it's easier to enter a DOI to search. You can refine the search results using Facets on the left side of the search results page. If you are on the table view, you can also search in a specific column by clicking the column title and enter the keywords.
If you still could not find your protocol in the search results, please help us by adding it into the system — it's easy. Create and publish your protocols at Protocols.io.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
