Fragmid
(Kit #
1000000237
)
Depositing Lab: John Doench
Fragmid is a modular toolkit that leverages Golden Gate cloning to enable the rapid creation of CRISPR vectors compatible with various delivery approaches, enzymes, and mechanisms. It also includes a set of positive control guides to facilitate the benchmarking of CRISPR technologies.
This kit will be sent as bacterial glycerol stocks in 96-well plate format.
Original Publication
Modular vector assembly enables rapid assessment of emerging CRISPR technologies. McGee AV, Liu YV, Griffith AL, Szegletes ZM, Wen B, Kraus C, Miller NW, Steger RJ, Velasco BE, Bosch JA, Zirin JD, Viswanatha R, Sontheimer EJ, Goodale A, Greene MA, Green TM, Doench JG. Cell Genomics. 2024 Mar 13;4(3):100519. doi: 10.1016/j.xgen.2024.100519. PubMed (Link opens in a new window) Article (Link opens in a new window)
Description
Fragmid consists of a comprehensive array of starting plasmids that can be combined in various configurations:
- The destination vectors are foundational backbones equipped with essential elements for delivery to target mammalian cells, including lentivirus, AAV, and PiggyBac-based transposon. Fragmid also supports delivery to Drosophila cells.
- The core of Fragmid's versatility lies in its modular fragments, which are categorized into several types based on their function with CRISPR systems:
- The guide cassettes contain RNA polymerase III promoters and constant RNA sequences for guide RNA association with Cas proteins. They can include validated targeting guides or cloning sites for custom guides.
- RNA polymerase II promoter fragments offer various promoter options to drive expression based on cell type and desired expression levels.
- The N-terminal and C-terminal domains include functional domains for different CRISPR applications, such as nuclear localization signals for knockout, transactivation domains for CRISPR activation (CRISPRa), and repression domains for CRISPR inhibition (CRISPRi).
- Cas proteins encompass a range of Cas enzymes from different species, including nuclease, nickase, and deactivated versions, as well as engineered variants with altered properties.
- The selection markers provide antibiotic resistance or visual markers for selection in eukaryotic cells.
- A basic set of pre-assembled vectors enables users to get started with CRISPR technology. These include vectors to express Cas proteins as well as vectors expressing positive control guides.
- The online portal is a user-friendly web platform that accompanies Fragmid, allowing users to browse available components, design custom CRISPR vectors by selecting from the modular fragments, and download the assembled vector maps: Fragmid Portal (Link opens in a new window) .
- Figure 1: Overview of Fragmid assembly process and resulting vector architecture.
Kit Documentation
Fragmid Inventory (CSV, 30 KB)How to Cite this Kit
These plasmids were created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which they were created, and include Addgene in the Materials and Methods of your future publications.
For your Materials and Methods section:
“The Fragmid Kit was a gift from John Doench (Addgene kit #1000000237).”
For your Reference section:
Modular vector assembly enables rapid assessment of emerging CRISPR technologies. McGee AV, Liu YV, Griffith AL, Szegletes ZM, Wen B, Kraus C, Miller NW, Steger RJ, Velasco BE, Bosch JA, Zirin JD, Viswanatha R, Sontheimer EJ, Goodale A, Greene MA, Green TM, Doench JG. Cell Genomics. 2024 Mar 13;4(3):100519. doi: 10.1016/j.xgen.2024.100519. PubMed (Link opens in a new window) Article (Link opens in a new window) .
Fragmid - #1000000237
- Resistance Color Key
Each circle corresponds to a specific antibiotic resistance in the kit plate map wells.
- Inventory
Searchable and sortable table of all plasmids in kit. The Well column links to its kit plate map on the right, as well as lists the plasmid well location in its plate. The Plasmid column links to a plasmid's individual web page.
- Kit Plate Map
96-well plate map for plasmid layout. Hovering over a well reveals the plasmid name, while clicking on a well opens the plasmid page.
Resistance Color Key
| Kanamycin | |
| Ampicillin |
Inventory
| Well | Plasmid | Resistance |
|---|---|---|
| Plate 1 / A / 1 | AA016 | Kanamycin |
| Plate 1 / A / 2 | AA017 | Kanamycin |
| Plate 1 / A / 3 | AA021 | Kanamycin |
| Plate 1 / A / 4 | AA022 | Kanamycin |
| Plate 1 / A / 5 | AA023 | Kanamycin |
| Plate 1 / A / 6 | AA054 | Kanamycin |
| Plate 1 / A / 7 | AA074 | Kanamycin |
| Plate 1 / A / 8 | AA083 | Kanamycin |
| Plate 1 / A / 9 | AA102 | Kanamycin |
| Plate 1 / A / 10 | AA107 | Kanamycin |
| Plate 1 / A / 11 | AA145 | Kanamycin |
| Plate 1 / A / 12 | AA151 | Kanamycin |
| Plate 1 / B / 1 | AA179 | Kanamycin |
| Plate 1 / B / 2 | AA232 | Kanamycin |
| Plate 1 / B / 3 | AA233 | Kanamycin |
| Plate 1 / B / 4 | AA238 | Kanamycin |
| Plate 1 / B / 5 | AA242 | Kanamycin |
| Plate 1 / B / 6 | AA243 | Kanamycin |
| Plate 1 / B / 7 | AA244 | Kanamycin |
| Plate 1 / B / 8 | AA246 | Kanamycin |
| Plate 1 / B / 9 | AA285 | Kanamycin |
| Plate 1 / B / 10 | AA286 | Kanamycin |
| Plate 1 / B / 11 | AA290 | Kanamycin |
| Plate 1 / B / 12 | AA310 | Kanamycin |
| Plate 1 / C / 1 | AA315 | Kanamycin |
| Plate 1 / C / 2 | AA320 | Kanamycin |
| Plate 1 / C / 3 | AA324 | Kanamycin |
| Plate 1 / C / 4 | AA331 | Kanamycin |
| Plate 1 / C / 5 | AA363 | Kanamycin |
| Plate 1 / C / 6 | AA364 | Kanamycin |
| Plate 1 / C / 7 | AA390 | Kanamycin |
| Plate 1 / C / 8 | AA400 | Kanamycin |
| Plate 1 / C / 9 | AA401 | Kanamycin |
| Plate 1 / C / 10 | AA403 | Kanamycin |
| Plate 1 / C / 11 | AA427 | Kanamycin |
| Plate 1 / C / 12 | AA435 | Kanamycin |
| Plate 1 / D / 1 | AA041 | Kanamycin |
| Plate 1 / D / 2 | AA043 | Kanamycin |
| Plate 1 / D / 3 | AA065 | Kanamycin |
| Plate 1 / D / 4 | AA066 | Kanamycin |
| Plate 1 / D / 5 | AA265 | Kanamycin |
| Plate 1 / D / 6 | AA294 | Kanamycin |
| Plate 1 / D / 7 | AA365 | Kanamycin |
| Plate 1 / D / 8 | AA366 | Kanamycin |
| Plate 1 / D / 9 | AA367 | Kanamycin |
| Plate 1 / D / 10 | AA368 | Kanamycin |
| Plate 1 / D / 11 | AA011 | Kanamycin |
| Plate 1 / D / 12 | AA012 | Kanamycin |
| Plate 1 / E / 1 | AA013 | Kanamycin |
| Plate 1 / E / 2 | AA018 | Kanamycin |
| Plate 1 / E / 3 | AA081 | Kanamycin |
| Plate 1 / E / 4 | AA088 | Kanamycin |
| Plate 1 / E / 5 | AA091 | Kanamycin |
| Plate 1 / E / 6 | AA122 | Kanamycin |
| Plate 1 / E / 7 | AA124 | Kanamycin |
| Plate 1 / E / 8 | AA125 | Kanamycin |
| Plate 1 / E / 9 | AA177 | Kanamycin |
| Plate 1 / E / 10 | AA195 | Kanamycin |
| Plate 1 / E / 11 | AA198 | Kanamycin |
| Plate 1 / E / 12 | AA295 | Kanamycin |
| Plate 1 / F / 1 | AA369 | Kanamycin |
| Plate 1 / F / 2 | AA370 | Kanamycin |
| Plate 1 / F / 3 | AA371 | Kanamycin |
| Plate 1 / F / 4 | AA413 | Kanamycin |
| Plate 1 / F / 5 | AA414 | Kanamycin |
| Plate 1 / F / 6 | AA416 | Kanamycin |
| Plate 1 / F / 7 | AA067 | Kanamycin |
| Plate 1 / F / 8 | AA068 | Kanamycin |
| Plate 1 / F / 9 | AA069 | Kanamycin |
| Plate 1 / F / 10 | AA070 | Kanamycin |
| Plate 1 / F / 11 | AA082 | Kanamycin |
| Plate 1 / F / 12 | AA104 | Kanamycin |
| Plate 1 / G / 1 | AA277 | Kanamycin |
| Plate 1 / G / 2 | AA278 | Kanamycin |
| Plate 1 / G / 3 | AA279 | Kanamycin |
| Plate 1 / G / 4 | AA007 | Kanamycin |
| Plate 1 / G / 5 | AA008 | Kanamycin |
| Plate 1 / G / 6 | AA020 | Kanamycin |
| Plate 1 / G / 7 | AA025 | Kanamycin |
| Plate 1 / G / 8 | AA026 | Kanamycin |
| Plate 1 / G / 9 | AA027 | Kanamycin |
| Plate 1 / G / 10 | AA028 | Kanamycin |
| Plate 1 / G / 11 | AA029 | Kanamycin |
| Plate 1 / G / 12 | AA030 | Kanamycin |
| Plate 1 / H / 1 | AA031 | Kanamycin |
| Plate 1 / H / 2 | AA032 | Kanamycin |
| Plate 1 / H / 3 | AA033 | Kanamycin |
| Plate 1 / H / 4 | AA034 | Kanamycin |
| Plate 1 / H / 5 | AA035 | Kanamycin |
| Plate 1 / H / 6 | AA048 | Kanamycin |
| Plate 1 / H / 7 | AA060 | Kanamycin |
| Plate 1 / H / 8 | AA061 | Kanamycin |
| Plate 1 / H / 9 | AA062 | Kanamycin |
| Plate 1 / H / 10 | AA063 | Kanamycin |
| Plate 1 / H / 11 | AA076 | Kanamycin |
| Plate 1 / H / 12 | AA156 | Kanamycin |
| Plate 2 / A / 1 | AA180 | Kanamycin |
| Plate 2 / A / 2 | AA181 | Kanamycin |
| Plate 2 / A / 3 | AA183 | Kanamycin |
| Plate 2 / A / 4 | AA201 | Kanamycin |
| Plate 2 / A / 5 | AA226 | Kanamycin |
| Plate 2 / A / 6 | AA296 | Kanamycin |
| Plate 2 / A / 7 | AA299 | Kanamycin |
| Plate 2 / A / 8 | AA301 | Kanamycin |
| Plate 2 / A / 9 | AA345 | Kanamycin |
| Plate 2 / A / 10 | AA349 | Kanamycin |
| Plate 2 / A / 11 | AA391 | Kanamycin |
| Plate 2 / A / 12 | AA436 | Kanamycin |
| Plate 2 / B / 1 | AA440 | Kanamycin |
| Plate 2 / B / 2 | AA009 | Kanamycin |
| Plate 2 / B / 3 | AA010 | Kanamycin |
| Plate 2 / B / 4 | AA019 | Kanamycin |
| Plate 2 / B / 5 | AA058 | Kanamycin |
| Plate 2 / B / 6 | AA092 | Kanamycin |
| Plate 2 / B / 7 | AA093 | Kanamycin |
| Plate 2 / B / 8 | AA095 | Kanamycin |
| Plate 2 / B / 9 | AA134 | Kanamycin |
| Plate 2 / B / 10 | AA141 | Kanamycin |
| Plate 2 / B / 11 | AA178 | Kanamycin |
| Plate 2 / B / 12 | AA184 | Kanamycin |
| Plate 2 / C / 1 | AA185 | Kanamycin |
| Plate 2 / C / 2 | AA197 | Kanamycin |
| Plate 2 / C / 3 | AA199 | Kanamycin |
| Plate 2 / C / 4 | AA200 | Kanamycin |
| Plate 2 / C / 5 | AA302 | Kanamycin |
| Plate 2 / C / 6 | AA332 | Kanamycin |
| Plate 2 / C / 7 | AA375 | Kanamycin |
| Plate 2 / C / 8 | AA428 | Kanamycin |
| Plate 2 / C / 9 | AA006 | Kanamycin |
| Plate 2 / C / 10 | AA014 | Kanamycin |
| Plate 2 / C / 11 | AA015 | Kanamycin |
| Plate 2 / C / 12 | AA050 | Kanamycin |
| Plate 2 / D / 1 | AA149 | Kanamycin |
| Plate 2 / D / 2 | AA163 | Kanamycin |
| Plate 2 / D / 3 | AA175 | Kanamycin |
| Plate 2 / D / 4 | AA176 | Kanamycin |
| Plate 2 / D / 5 | AA266 | Kanamycin |
| Plate 2 / D / 6 | AA267 | Kanamycin |
| Plate 2 / D / 7 | AA276 | Kanamycin |
| Plate 2 / D / 8 | AA333 | Kanamycin |
| Plate 2 / D / 9 | AA334 | Kanamycin |
| Plate 2 / D / 10 | AA335 | Kanamycin |
| Plate 2 / D / 11 | AA406 | Kanamycin |
| Plate 2 / D / 12 | AA303 | Kanamycin |
| Plate 2 / E / 1 | AA304 | Kanamycin |
| Plate 2 / E / 2 | AA269 | Kanamycin |
| Plate 2 / E / 3 | AA271 | Kanamycin |
| Plate 2 / E / 4 | pRDA_512 | Ampicillin |
| Plate 2 / E / 5 | pRDA_575 | Ampicillin |
| Plate 2 / E / 6 | pRDA_722 | Ampicillin |
| Plate 2 / E / 7 | pRDA_789 | Ampicillin |
| Plate 2 / E / 8 | pRDA_791 | Ampicillin |
| Plate 2 / E / 9 | pRDA_889 | Ampicillin |
| Plate 2 / E / 10 | pRDB_051 | Ampicillin |
| Plate 2 / E / 11 | pRDB_052 | Ampicillin |
| Plate 2 / E / 12 | pRDB_053 | Ampicillin |
| Plate 2 / F / 1 | pRDA_792 | Ampicillin |
| Plate 2 / F / 2 | pRDA_832 | Ampicillin |
| Plate 2 / F / 3 | pRDA_833 | Ampicillin |
| Plate 2 / F / 4 | pRDA_834 | Ampicillin |
| Plate 2 / F / 5 | pRDA_836 | Ampicillin |
| Plate 2 / F / 6 | pRDB_118 | Ampicillin |
| Plate 2 / F / 7 | pRDB_156 | Ampicillin |
| Plate 2 / F / 8 | pRDB_161 | Ampicillin |
| Plate 2 / F / 9 | pRDB_162 | Ampicillin |
| Plate 2 / F / 10 | pRDB_166 | Ampicillin |
| Plate 2 / F / 11 | pRDA_936 | Ampicillin |
| Plate 2 / F / 12 | pRDB_131 | Ampicillin |
| Plate 2 / G / 1 | pRDB_054 | Ampicillin |
| Plate 2 / G / 2 | pRDA_734 | Ampicillin |
| Plate 2 / G / 3 | pRDA_816 | Ampicillin |
| Plate 2 / G / 4 | pMV_AA090 | Ampicillin |
| Plate 2 / G / 5 | pRDA_831 | Ampicillin |
| Plate 2 / G / 6 | pRDA_662 | Ampicillin |
| Plate 2 / G / 7 | pRDB_181 | Ampicillin |
| Plate 2 / G / 8 | pRDB_182 | Ampicillin |
| Plate 2 / G / 9 | pMV_AA088 | Ampicillin |
| Plate 2 / G / 10 | pMV_AA089 | Ampicillin |
| Plate 2 / G / 11 | pMV_AA091 | Ampicillin |
| Plate 2 / G / 12 | pMV_AA050 | Ampicillin |