{"_id":"54ecf59b172d6b2b003b3178","parentDoc":null,"user":"54e3d35e464a9c3700f7ca7f","project":"5476bf0f817e8d080031f988","version":{"_id":"5476bf10817e8d080031f98b","__v":17,"project":"5476bf0f817e8d080031f988","createdAt":"2014-11-27T06:05:04.263Z","releaseDate":"2014-11-27T06:05:04.263Z","categories":["5476bf10817e8d080031f98c","5477c46cf3736008009e9eb5","5477c474f3736008009e9eb6","5477c47ef3736008009e9eb7","5477c48ff3736008009e9eb8","5477c4948deb230800808bf0","54e68328154f8e0d0007b55c","54e90194c8e0c00d007ac061","54eed2275bf74a0d00ef4076","54f7a7be0a3cbb0d00d666fb","559b0ebf7ae7f80d0096d871","55d697f9ae529e0d00d34f03","562d4dcc8c6e5a0d00d6ed1d","562e591c4376430d006f17e0","568f0e73bdb9260d00149d8c","5719542aac1e2e0e001834c6","57a14a8ed778850e0047e230"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"__v":19,"category":{"_id":"54e68328154f8e0d0007b55c","project":"5476bf0f817e8d080031f988","version":"5476bf10817e8d080031f98b","__v":8,"pages":["54e68e63a43fe13500db387a","54e68e98bdcbdc21000d55e6","54e6ca051415460d009fc118","54ecf59b172d6b2b003b3178","54ecf790172d6b2b003b317a","54eec2f35bf74a0d00ef4063","56d10611376b040b005b3135","56e36cf4f7d7a71700234792"],"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-02-20T00:43:20.640Z","from_sync":false,"order":3,"slug":"design-rules-limitations","title":"Developing on Transcriptic"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2015-02-24T22:05:15.966Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":1,"body":"[block:callout]\n{\n  \"type\": \"warning\",\n  \"body\": \"How well you understand the limitations described here will be directly related to your success on Transcriptic Platform.\",\n  \"title\": \"This section is extremely important. Please do not skip it.\"\n}\n[/block]\nThough we often use the analogy of \"cloud computing\" in describing Transcriptic, biological protocols are sufficiently sensitive that the analogy only goes so far. Transcriptic is not a commodity platform, and you do need to understand some implementation details in order to make best use of it. A better analogy might be semiconductor fabrication: when you select a foundry partner, you receive a large set of design rules that must be followed to ensure success in that specific foundry's process. That foundry model is similar to how Transcriptic Platform operates. **The protocols that you run on Transcriptic will not be one-to-one ports of the protocols you're used to running by hand at your own bench, and they'll even be different from what you might be used to running on other automation.**\n\nIf you understand and take into account the design rules in the following sections, though, you will be able to write reliable, efficient protocols that require little ongoing debugging.\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Guide To Liquid Handling\"\n}\n[/block]\nLiquid handling is a critical part of any biological protocol. It's also deceptively complex. There are a large number of factors that affect the accuracy of a liquid handling operation. We've found that it works best to understand how liquid handling works holistically rather than as disconnected parts used to solve specific problems. This section attempts to describe in detail each of those factors and their cumulative effect on the results of a liquid handling operation.\n\n## Factors That Matter When Handling Liquids\nThere are four types of liquid handlers at Transcriptic: Tecan air displacement pipettors (Tecan ADP), Agilent multi-channel air displacement pipettors, Labcyte Echo 525 Acoustic Droplet Ejection (Echo ADE) instruments, and manual pipettors operated by lab technicians. Each are used for different types of liquid handling and each have strengths and limitations.\n\nWhen working with air displacement pipettors and small volumes (< 10 μl), the ordering of liquid handling operations is important. Small volumes can be dispensed into large volumes with precision (± 5%), but dispensing small volumes into empty wells will be unreliable (± 20% or more). Similarly, aspiration is only precise if the entire bottom of the well is submerged, creating a \"dead volume\". Dead volumes are intrinsic to all forms of automated liquid handling, including ADE. Review dead volumes for each container type on the [Containers page](doc:containers)  If an instruction asks to aspirate a volume that exceeds the \"alive\" volume of the well, the aspiration must be done manually, creating a substantial performance hit. This option may be removed entirely in the future, causing such aspirations to simply be illegal instructions.\n\nSpecial considerations are required when transferring small volumes of solutions that contain large or heavy components such as cells. This is due to the fact that acoustic droplet ejection transfers from the meniscus of the liquid, and components of the solution that will settle to the bottom of the well may not be transferred efficiently. Further, though our ADE process is configured to use 25 nl droplets (the largest droplet size available), the physics of the transfer may result in a bias against transferring physically large solution components. Ensure such solutions are well mixed before attempting the transfer.\n\nAcoustic liquid handling is a gentle process and should not harm samples; in fact, it's considerably more gentle than pipetting-based liquid handling due to the absence of shear forces at the tip interface.\n\n## Distribute, Consolidate, Transfer, Mix\nThe `pipette` instruction's `groups` has four different modes:\n\n`transfer`: one `from`, one `to`  \n`distribute`: one `from`, many `to`  \n`consolidate`: many `from`, one `to`  \n`mix`: many `well`\n    \nDue to the physics of liquid handling, slight adjustments to the process are needed achieve the best possible precision and accuracy. Transcriptic will automatically perform some of these optimizations under the hood, but it's important for you to understand what is happening.\n\nIn a transfer or batch transfer operation, the exact volume commanded will be aspirated and dispensed unless the requested volume is below 5 μl, in which case the requested volume + 10% will be aspirated and half of the predicted overage will be immediately dispensed back into the source well.\n\nIn a distribute operation, slightly more than the commanded volume (~ 7%) is aspirated and a small amount (~ 3%) is immediately dispensed back into the source. A small residual volume is expected to remain after all of the dispenses into the destination wells, which is discarded. This process allows pipetting accuracy ± 5% for volumes down to 5 μl.\n\nA consolidate operation does not expose a tip to more than one source well—the performance gains come when a multichannel (e.g., span 8) pipetting system is used.\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Plate Reformatting\"\n}\n[/block]\nBecause of the aforementioned liquid handling constraints, sample \"reformatting\"—the process of moving samples from one container or layout in a container to another—is an expensive process. You must put thought into the flow of your protocol to avoid unnecessary container format changes.\n\nIf you must do this (for example, to transfer an aliquot from a V-bottom plate to a flat-bottom plate for an analytical reading, you should use consider using the [stamp](doc:multichannel-liquid-handling-stamping) instruction.","excerpt":"","slug":"liquid-handling-guide","type":"basic","title":"Liquid Handling & Plate Reformatting"}

Liquid Handling & Plate Reformatting


[block:callout] { "type": "warning", "body": "How well you understand the limitations described here will be directly related to your success on Transcriptic Platform.", "title": "This section is extremely important. Please do not skip it." } [/block] Though we often use the analogy of "cloud computing" in describing Transcriptic, biological protocols are sufficiently sensitive that the analogy only goes so far. Transcriptic is not a commodity platform, and you do need to understand some implementation details in order to make best use of it. A better analogy might be semiconductor fabrication: when you select a foundry partner, you receive a large set of design rules that must be followed to ensure success in that specific foundry's process. That foundry model is similar to how Transcriptic Platform operates. **The protocols that you run on Transcriptic will not be one-to-one ports of the protocols you're used to running by hand at your own bench, and they'll even be different from what you might be used to running on other automation.** If you understand and take into account the design rules in the following sections, though, you will be able to write reliable, efficient protocols that require little ongoing debugging. [block:api-header] { "type": "basic", "title": "Guide To Liquid Handling" } [/block] Liquid handling is a critical part of any biological protocol. It's also deceptively complex. There are a large number of factors that affect the accuracy of a liquid handling operation. We've found that it works best to understand how liquid handling works holistically rather than as disconnected parts used to solve specific problems. This section attempts to describe in detail each of those factors and their cumulative effect on the results of a liquid handling operation. ## Factors That Matter When Handling Liquids There are four types of liquid handlers at Transcriptic: Tecan air displacement pipettors (Tecan ADP), Agilent multi-channel air displacement pipettors, Labcyte Echo 525 Acoustic Droplet Ejection (Echo ADE) instruments, and manual pipettors operated by lab technicians. Each are used for different types of liquid handling and each have strengths and limitations. When working with air displacement pipettors and small volumes (< 10 μl), the ordering of liquid handling operations is important. Small volumes can be dispensed into large volumes with precision (± 5%), but dispensing small volumes into empty wells will be unreliable (± 20% or more). Similarly, aspiration is only precise if the entire bottom of the well is submerged, creating a "dead volume". Dead volumes are intrinsic to all forms of automated liquid handling, including ADE. Review dead volumes for each container type on the [Containers page](doc:containers) If an instruction asks to aspirate a volume that exceeds the "alive" volume of the well, the aspiration must be done manually, creating a substantial performance hit. This option may be removed entirely in the future, causing such aspirations to simply be illegal instructions. Special considerations are required when transferring small volumes of solutions that contain large or heavy components such as cells. This is due to the fact that acoustic droplet ejection transfers from the meniscus of the liquid, and components of the solution that will settle to the bottom of the well may not be transferred efficiently. Further, though our ADE process is configured to use 25 nl droplets (the largest droplet size available), the physics of the transfer may result in a bias against transferring physically large solution components. Ensure such solutions are well mixed before attempting the transfer. Acoustic liquid handling is a gentle process and should not harm samples; in fact, it's considerably more gentle than pipetting-based liquid handling due to the absence of shear forces at the tip interface. ## Distribute, Consolidate, Transfer, Mix The `pipette` instruction's `groups` has four different modes: `transfer`: one `from`, one `to` `distribute`: one `from`, many `to` `consolidate`: many `from`, one `to` `mix`: many `well` Due to the physics of liquid handling, slight adjustments to the process are needed achieve the best possible precision and accuracy. Transcriptic will automatically perform some of these optimizations under the hood, but it's important for you to understand what is happening. In a transfer or batch transfer operation, the exact volume commanded will be aspirated and dispensed unless the requested volume is below 5 μl, in which case the requested volume + 10% will be aspirated and half of the predicted overage will be immediately dispensed back into the source well. In a distribute operation, slightly more than the commanded volume (~ 7%) is aspirated and a small amount (~ 3%) is immediately dispensed back into the source. A small residual volume is expected to remain after all of the dispenses into the destination wells, which is discarded. This process allows pipetting accuracy ± 5% for volumes down to 5 μl. A consolidate operation does not expose a tip to more than one source well—the performance gains come when a multichannel (e.g., span 8) pipetting system is used. [block:api-header] { "type": "basic", "title": "Plate Reformatting" } [/block] Because of the aforementioned liquid handling constraints, sample "reformatting"—the process of moving samples from one container or layout in a container to another—is an expensive process. You must put thought into the flow of your protocol to avoid unnecessary container format changes. If you must do this (for example, to transfer an aliquot from a V-bottom plate to a flat-bottom plate for an analytical reading, you should use consider using the [stamp](doc:multichannel-liquid-handling-stamping) instruction.