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Merge pull request #4255 from Opentrons/nextera_xt_fix
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updated pdf link
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john-c-lynch authored Nov 30, 2022
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2 changes: 1 addition & 1 deletion protoBuilds/illumina-nextera-XT-library-prep-part1/README.json
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"markdown": {
"author": "[Opentrons](https://opentrons.com/)\n\n",
"categories": "* Featured\n * NGS Library Prep: Illumina Nextera XT\n\n",
"description": "Part 1 of 4: Tagment Genomic DNA and Amplify Libraries\n\nLinks:\n* [Part 1: Tagment and Amplify](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n* [Part 2: Clean Up Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part2)\n* [Part 3: Normalize Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part3)\n* [Part 4: Pool Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part4)\n\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol described by the [Illumina Reference Guide](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-03.pdf).\n\nThis is part 1 of the protocol, which includes the steps (1) Tagment Genomic DNA and (2) Amplify Libraries.\n\nThe tagmentation step uses Nextera transposase to fragment DNA into sizes suitable for sequencing, and then tags the DNA with adapter sequences. The library amplification step increases the yield of the tagmented DNA using PCR. PCR adds the Index 1 (i7), Index 2 (i5), and full adapter sequences to the tagmented DNA from the previous step. This protocol assumes you are taking your plate off the OT-2 and thermocycling on a stand-alone PCR machine according to the [Illumina Reference Guide](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-05.pdf).\n\nAfter the two steps carried out in this protocol, you can safely stop work and return to it at a later point. If you are stopping, seal the plate and store at 2\u00b0C to 8\u00b0C for up to 2 days.\n\n",
"description": "Part 1 of 4: Tagment Genomic DNA and Amplify Libraries\n\nLinks:\n* [Part 1: Tagment and Amplify](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n* [Part 2: Clean Up Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part2)\n* [Part 3: Normalize Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part3)\n* [Part 4: Pool Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part4)\n\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol described by the [Illumina Reference Guide](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-06.pdf).\n\nThis is part 1 of the protocol, which includes the steps (1) Tagment Genomic DNA and (2) Amplify Libraries.\n\nThe tagmentation step uses Nextera transposase to fragment DNA into sizes suitable for sequencing, and then tags the DNA with adapter sequences. The library amplification step increases the yield of the tagmented DNA using PCR. PCR adds the Index 1 (i7), Index 2 (i5), and full adapter sequences to the tagmented DNA from the previous step. This protocol assumes you are taking your plate off the OT-2 and thermocycling on a stand-alone PCR machine according to the [Illumina Reference Guide](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-05.pdf).\n\nAfter the two steps carried out in this protocol, you can safely stop work and return to it at a later point. If you are stopping, seal the plate and store at 2\u00b0C to 8\u00b0C for up to 2 days.\n\n",
"internal": "bU7eUGEh\n872\n",
"notes": "* 2-mL Tuberack Reagent Setup:\n * Amplicon Tagment Mix: **A1**\n * Tagment DNA Buffer: **B1**\n * Neutralize Tagment Buffer: **C1**\n * Nextera PCR Master Mix: **D1**\n* Review the reference guide before proceeding to confirm kit contents and make sure you have the required equipment and consumables.\n\n",
"preview": "With this series of protocols and the [Opentrons Magnetic Module](https://shop.opentrons.com/products/magdeck), your robot can complete a library prep using the [Illumina Nextera XT DNA Library Prep Kit](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-03.pdf). This library prep protocol comes in four parts: Tagment and Amplify, Clean Up Libraries, Normalize Libraries, and Pool Libraries.\n\n",
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2 changes: 1 addition & 1 deletion protoBuilds/illumina-nextera-XT-library-prep-part2/README.json
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"markdown": {
"author": "[Opentrons](https://opentrons.com/)\n\n",
"categories": "* Featured\n * NGS Library Prep: Illumina Nextera XT\n\n",
"description": "Part 2 of 4: Clean Up Libraries\n\nLinks:\n* [Part 1: Tagment and Amplify](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n* [Part 2: Clean Up Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part2)\n* [Part 3: Normalize Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part3)\n* [Part 4: Pool Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part4)\n\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol describe by the [Illumina Reference Guide](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-05.pdf).\n\nThis is Part 2 of the protocol, which consists of just step (3) of the overall process: clean up libraries. This step uses AMPure XP beads to purify the library DNA and remove short library fragments after the previous step, library amplification.\n\nAfter this step, it is safe to stop the workflow and return to it at a later point. If you are stopping, seal the plate and store at -15\u00b0C to -25\u00b0C for up to seven days.\n\n---\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [[email protected]](mailto:[email protected])\n\n* [Opentrons OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2)\n* [Opentrons OT-2 Run App (Version 3.15.0 or later)](https://opentrons.com/ot-app/)\n* [Opentrons P300 or P50 Pipette (Single or 8-Channel)](https://shop.opentrons.com/collections/ot-2-pipettes) and corresponding [Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n* [Opentrons Magnetic Module](https://shop.opentrons.com/collections/hardware-modules/products/magdeck)\n* [Bio-Rad 96-Well Plate, 200\u03bcl](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr) containing samples from [Part 1](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n* [Bio-Rad 96-Well Plate, 200\u03bcl](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr), clean and empty (x2)\n* [USA Scientific 12-Channel Reservoir](https://labware.opentrons.com/usascientific_12_reservoir_22ml?category=reservoir)\n* [Nextera XT DNA Library Prep Kit](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-xt-dna.html)\n\nFor more detailed information on compatible labware, please visit our [Labware Library](https://labware.opentrons.com/).\n\n\n---\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\n\nThis protocol requires specific labware in a specific set-up.\n\nSlot 1: [Bio-Rad Plate](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr?category=wellPlate) (clean and empty); final elution will be transferred to this plate.\n\nSlot 2: [USA Scientific 12-Channel Reservoir](https://labware.opentrons.com/usascientific_12_reservoir_22ml?category=reservoir)\n* A1: Resuspension Buffer\n* A2: AMPure XP Beads\n* A3: 80% Ethanol\n* A4: 80% Ethanol (if needed)\n* A5: 80% Ethanol (if needed)\n* A9: Liquid Waste\n* A10: Liquid Waste\n* A11: Liquid Waste\n* A12: Liquid Waste\n\nSlot 4: [Magnetic Module](https://shop.opentrons.com/collections/hardware-modules/products/magdeck) with [Bio-Rad Plate](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr?category=wellPlate) (clean and empty)\n\nSlot 5: [Bio-Rad Plate](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr) containing samples from [Part 1](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n\nSlot 6: [Opentrons Tip Rack](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n\nSlot 7: [Opentrons Tip Rack](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n\nSlot 8: [Opentrons Tip Rack](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n* Note: If your protocol requires more tips due to the parameters you set, you will need to fill subsequent slots with tip racks.\n\n\nUsing the customization fields below, set up your protocol.\n* Pipette Model: Select which pipette (P50/P300; Single/8-Channel) you will use for this protocol.\n* Pipette Mount: Specify which mount your single-channel pipette is on (left or right).\n* Magnetic Module Gen: Specify which Magnetic Module is in use\n* Number of Samples: Select the number of samples (1-96) to be run in the protocol.\n* Initial Product Volume (\u00b5l): Select the starting volume of PCR product to be used in the protocol.\n* Bead Ratio: Select the bead ratio. 1.8 is recommended for small (300-500 bp) inputs, and 0.6 is recommended for larger (>500 bp) samples. Please see [documentation](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-05.pdf) for more information.\n* Resuspension Buffer Volume (\u00b5L): Specify how much Resuspension Buffer is added to the wells.\n* Final PCR Product Volume (\u00b5L): Specify the final elution volume to be transferred.\n* Dry Time (minutes): Specify how long (in minutes) you would like to let the beads dry after the wash steps and before adding the resuspension buffer.\n\n\n\n\n\n",
"description": "Part 2 of 4: Clean Up Libraries\n\nLinks:\n* [Part 1: Tagment and Amplify](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n* [Part 2: Clean Up Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part2)\n* [Part 3: Normalize Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part3)\n* [Part 4: Pool Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part4)\n\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol describe by the [Illumina Reference Guide](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-06.pdf).\n\nThis is Part 2 of the protocol, which consists of just step (3) of the overall process: clean up libraries. This step uses AMPure XP beads to purify the library DNA and remove short library fragments after the previous step, library amplification.\n\nAfter this step, it is safe to stop the workflow and return to it at a later point. If you are stopping, seal the plate and store at -15\u00b0C to -25\u00b0C for up to seven days.\n\n---\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [[email protected]](mailto:[email protected])\n\n* [Opentrons OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2)\n* [Opentrons OT-2 Run App (Version 3.15.0 or later)](https://opentrons.com/ot-app/)\n* [Opentrons P300 or P50 Pipette (Single or 8-Channel)](https://shop.opentrons.com/collections/ot-2-pipettes) and corresponding [Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n* [Opentrons Magnetic Module](https://shop.opentrons.com/collections/hardware-modules/products/magdeck)\n* [Bio-Rad 96-Well Plate, 200\u03bcl](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr) containing samples from [Part 1](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n* [Bio-Rad 96-Well Plate, 200\u03bcl](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr), clean and empty (x2)\n* [USA Scientific 12-Channel Reservoir](https://labware.opentrons.com/usascientific_12_reservoir_22ml?category=reservoir)\n* [Nextera XT DNA Library Prep Kit](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-xt-dna.html)\n\nFor more detailed information on compatible labware, please visit our [Labware Library](https://labware.opentrons.com/).\n\n\n---\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\n\nThis protocol requires specific labware in a specific set-up.\n\nSlot 1: [Bio-Rad Plate](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr?category=wellPlate) (clean and empty); final elution will be transferred to this plate.\n\nSlot 2: [USA Scientific 12-Channel Reservoir](https://labware.opentrons.com/usascientific_12_reservoir_22ml?category=reservoir)\n* A1: Resuspension Buffer\n* A2: AMPure XP Beads\n* A3: 80% Ethanol\n* A4: 80% Ethanol (if needed)\n* A5: 80% Ethanol (if needed)\n* A9: Liquid Waste\n* A10: Liquid Waste\n* A11: Liquid Waste\n* A12: Liquid Waste\n\nSlot 4: [Magnetic Module](https://shop.opentrons.com/collections/hardware-modules/products/magdeck) with [Bio-Rad Plate](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr?category=wellPlate) (clean and empty)\n\nSlot 5: [Bio-Rad Plate](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr) containing samples from [Part 1](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n\nSlot 6: [Opentrons Tip Rack](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n\nSlot 7: [Opentrons Tip Rack](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n\nSlot 8: [Opentrons Tip Rack](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n* Note: If your protocol requires more tips due to the parameters you set, you will need to fill subsequent slots with tip racks.\n\n\nUsing the customization fields below, set up your protocol.\n* Pipette Model: Select which pipette (P50/P300; Single/8-Channel) you will use for this protocol.\n* Pipette Mount: Specify which mount your single-channel pipette is on (left or right).\n* Magnetic Module Gen: Specify which Magnetic Module is in use\n* Number of Samples: Select the number of samples (1-96) to be run in the protocol.\n* Initial Product Volume (\u00b5l): Select the starting volume of PCR product to be used in the protocol.\n* Bead Ratio: Select the bead ratio. 1.8 is recommended for small (300-500 bp) inputs, and 0.6 is recommended for larger (>500 bp) samples. Please see [documentation](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-05.pdf) for more information.\n* Resuspension Buffer Volume (\u00b5L): Specify how much Resuspension Buffer is added to the wells.\n* Final PCR Product Volume (\u00b5L): Specify the final elution volume to be transferred.\n* Dry Time (minutes): Specify how long (in minutes) you would like to let the beads dry after the wash steps and before adding the resuspension buffer.\n\n\n\n\n\n",
"internal": "bU7eUGEh\n872\n",
"modules": "* [Magnetic Module](https://opentrons.com/modules)\n\n",
"notes": "If you\u2019d like to request a protocol supporting multiple plates or require other changes to this script, please fill out our [Protocol Request Form](https://opentrons-protocol-dev.paperform.co/). You can also modify the Python file directly by following our [API Documentation](https://docs.opentrons.com/v2/). If you\u2019d like to chat with an applications engineer about changes, please contact us at [[email protected]](mailto:[email protected]).\n\n",
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