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[]
[null,null,"PROTOCOL PLANNER",null,null,null,null,null,null,null,"CG000780"]
[null,null,"GEM-X Flex Gene Expression – Protocol Planner",null,null,null,null,null,null,null,"Rev A"]
[]
[]
["Introduction"]
[null,"GEM-X Flex Gene Expression offers comprehensive scalable solutions to measure gene and protein expression in samples that are fixed with formaldehyde. This document provides workflow overviews, document resources, reagents, and consumables for the GEM-X Flex protocols. This document also provides guidance on selecting the appropriate sample preparation and library construction protocols for different workflows. An overview of the GEM-X Flex data analysis is also included in this document. \nThe 10x Genomics GEM-X Flex Gene Expression Reagent Kits are not listed in this document."]
[]
[null,"Copy-Paste Guidelines:\nThe sheet is protected to prevent altering the content. In order to copy-paste, right click to select a cell's text."]
[null,"Printing Guidelines:\nThe print area has been set for each tab in this document. Go to Print. For orientation, select \"Portrait.\" For scaling, select \"Fit all columns to one page.\" \nTo print the entire workbook, Go to Print and select \"Print Entire Workbook\" under settings. \nTo create a pdf document, go to Print and select \"Adobe PDF\" as the printer. Do not go to \"Save as Adobe PDF.\""]
[]
["Workflow Overview"]
[]
[null,"Figure 1. Samples are either labeled with antibody-oligonucleotide conjugates and fixed (gene and protein expression workflows) or are directly fixed (gene expression only workflows). Fixed samples are then hybridized to probe sets. For gene & protein expression workflows, additional barcodes are added. The hybridized samples may be processed individually (singleplex workflow) or pooled with up to 16 samples (multiplex workflow). During GEM generation, the probe sets are ligated and extended to incorporate unique barcodes. Sequencing libraries are then prepared, sequenced, and analyzed."]
[]
[]
["GEM-X Flex Protocol Selection"]
[null,"This section provides guidance on choosing the appropriate documents for the following GEM-X Flex workflows. A high-level overview of protcol timing and stop options is also included."]
[]
[null,"1. Singleplexing Workflow – Gene Expression Only\n    "]
[null,"2. Multiplexing Workflow – Gene Expression Only\n    "]
[null,"3. Singleplexing Workflow – Gene & Protein Expression \n "]
[null,"4. Multiplexing Workflow – Gene & Protein Expression\n    "]
[]
[null,"Steps",null,null,null,null,"Timing",null,"Stop & Store"]
[null,"Workflows 1 & 2: Gene Expression Only"]
[null,"Sample Preparation",null,null,null,null,"variable",null,"4°C ≤1 week/-80°C ≤12 months"]
[null,"   • Fix Cells/Nuclei Suspension (CG000782)\n   • Tissue Fixation & Dissociation (CG000783)\n   • FFPE - Sample Preparation (CG000784)\n   • Blood Fixation & Cell Isolation (CG000785)\n   "]
[null,"Library Construction",null,null,null,null,"2 days (see Library Construction: Protocol Steps & Timing steps below for details)",null,"See Library Construction: Protocol Steps & Timing below for stop options"]
[null,"1. Singleplexing Workflow\n   • GEM-X Flex – Singleplexed Samples (CG000786)\nOR\n2. Multiplexing Workflow\n   • GEM-X Flex – Multiplexed Samples (CG000787)"]
[]
[null,"Steps",null,null,null,null,"Timing",null,"Stop & Store"]
[null,"Workflows 3 & 4: Gene & Protein Expression using Barcode Oligo Capture"]
[null,"Sample Labeling",null,null,null,null,"2–3 h",null,"-80°C ≤12 months after brief fixation during intracellular protein labeling"]
[null,"   • Cell Surface & Intracellular Protein Labeling (CG000781) "]
[null,"Sample Preparation",null,null,null,null,"variable",null,"4°C ≤1 week/-80°C ≤12 months"]
[null,"   • Fix Cells/Nuclei Suspension (CG000782)"]
[null,"Library Construction",null,null,null,null,"2 days (see Library Construction: Protocol Steps & Timing steps below for details)",null,"See Library Construction: Protocol Steps & Timing below for stop options"]
[null,"3. Singleplexing Workflow\n   • GEM-X Flex – Singleplexed Samples with Feature Barcode \n      technology for Protein using Barcode Oligo Capture (CG000788)\nOR\n4. Multiplexing Workflow\n   • GEM-X Flex – Multiplexed Samples with Feature Barcode \n      technology for Protein using Barcode Oligo Capture (CG000789)"]
[]
[]
["Workflow 1: GEM-X Flex Gene Expression for Singleplexed Samples"]
[]
[]
[]
["Document Resources for Workflow 1"]
[null,"Steps",null,"Document",null,null,null,null,null,"Doc Number"]
[null,"Sample Preparation\nDetailed guidance for\nsample fixation or isolation of cells from fixed sections. ",null,"Sample Fixation\nFix single cell & nuclei suspensions",null,null,null,null,null,"Demonstrated Protocol\nCG000782"]
[null,null,null,"Tissue Fixation\nFix & dissociate tissues",null,null,null,null,null,"Demonstrated Protocol\nCG000783"]
[null,null,null,"Sample Preparation – FFPE Samples  \nIsolate nuclei from FFPE sections",null,null,null,null,null,"Demonstrated Protocol\nCG000784"]
[null,null,null,"Blood Fixation\nFix blood and isolate cells",null,null,null,null,null,"Demonstrated Protocol\nCG000785"]
[null,"Library Construction\nDetailed steps & guidance on probe hybridization, GEM generation & library\nconstruction.",null,"Library Construction\nConstruct GEM-X Flex Gene Expression library",null,null,null,null,null,"User Guide \nCG000786"]
[]
[]
["Workflow 2: GEM-X Flex Gene Expression for Multiplexed Samples"]
[]
[]
[]
["Document Resources for Workflow 2"]
[null,"Steps",null,"Document",null,null,null,null,null,"Doc Number"]
[null,"Sample Preparation\nDetailed guidance for\nsample fixation or isolation of cells from fixed sections. ",null,"Sample Fixation\nFix single cell & nuclei suspensions",null,null,null,null,null,"Demonstrated Protocol\nCG000782"]
[null,null,null,"Tissue Fixation\nFix & dissociate tissues",null,null,null,null,null,"Demonstrated Protocol\nCG000783"]
[null,null,null,"Sample Preparation – FFPE Samples  \nIsolate nuclei from FFPE sections",null,null,null,null,null,"Demonstrated Protocol\nCG000784"]
[null,null,null,"Blood Fixation\nFix cells from blood",null,null,null,null,null,"Demonstrated Protocol\nCG000785"]
[null,"Library Construction\nDetailed steps & guidance on probe hybridization, GEM generation & library\nconstruction.",null,"Library Construction\nConstruct GEM-X Flex Gene Expression libraries for multiplexed samples",null,null,null,null,null,"User Guide \nCG000787"]
[]
[]
["Workflow 3: GEM-X Flex Gene & Protein Expression for Singleplexed Samples using Barcode \n                     Oligo Capture"]
[]
[]
[]
["Document Resources for Workflow 3"]
[null,"Steps",null,"Document",null,null,null,null,null,"Doc Number"]
[null,"Sample Preparation\nDetailed guidance for\nsample labeling and\nfixation.",null,"Cell Surface & Intracellular Protein Labeling\nLabel cells with cell surface and intracellular antibody-oligonucleotide conjugates ",null,null,null,null,null,"Demonstrated Protocol\nCG000781"]
[null,null,null,"Sample Fixation\nFix single cell & nuclei suspensions",null,null,null,null,null,"Demonstrated Protocol\nCG000782"]
[null,"Library Construction\nDetailed steps & guidance on probe hybridization, GEM generation & library\nconstruction.",null,"Library Construction\nConstruct GEM-X Flex Gene & Protein Expression libraries",null,null,null,null,null,"User Guide \nCG000788"]
[]
[]
["Workflow 4: GEM-X Flex Gene & Protein Expression for Multiplexed Samples using Barcode \n                     Oligo Capture"]
[]
[]
[]
["Document Resources for Workflow 4"]
[null,"Steps",null,"Document",null,null,null,null,null,"Doc Number"]
[null,"Sample Preparation\nDetailed guidance for\nsample labeling and\nfixation.",null,"Cell Surface & Intracellular Protein Labeling\nLabel cells with cell surface and intracellular antibody-oligonucleotide conjugates ",null,null,null,null,null,"Demonstrated Protocol\nCG000781"]
[null,null,null,"Sample Fixation\nFix single cell & nuclei suspensions",null,null,null,null,null,"Demonstrated Protocol\nCG000782"]
[null,"Library Construction\nDetailed steps & guidance on probe hybridization, GEM generation & library\nconstruction.",null,"Library Construction\nConstruct GEM-X Flex Gene & Protein Expression libraries for multiplexed samples",null,null,null,null,null,"User Guide \nCG000789"]
[]
["Additional Resources (Workflows 1-4)"]
[null,"Steps",null,"Document",null,null,null,null,null,"Doc Number"]
[null,"Using Custom Probes\n",null,"Custom Probe Design \nGuidance for designing and using custom probes for Gene Expression Flex singleplexed and multiplexed experiments",null,null,null,null,null,"Technical Note\nCG000621"]
[null,"CRISPR Screening with GEM-X Flex Assay",null,"Suggested workflow modifications for CRISPR Screening with the Gene Expression Flex assay",null,null,null,null,null,"Link here"]
[null,null,null,"General design guidance for custom probes for CRISPR guide capture",null,null,null,null,null,"Link here"]
[null,null,null,"Pooling calculations for setting up the probe hybridization",null,null,null,null,null,"Link here"]
[null,null,null,"Setting up a Flex + CRISPR Cell Ranger run",null,null,null,null,null,"Link here"]
[]
["Library Construction: Protocol Steps & Timing (for Workflows 1-4)"]
[null,"Steps",null,null,null,null,"Timing",null,"Stop & Store"]
[null,"Step 1: Probe Hybridization"]
[null,1.1000000000000001,"Probe Hybridization",null,null,null,"16-24 h"]
[null,"Step 2: Post-Hybridization Washing"]
[null,2.1,"Post-Hybridization Pool* & Wash",null,null,null,"60–90 min",null,"-80°C ≤12 months"]
[null,"Step 3: GEM Generation & Barcoding"]
[null,3.1,"Prepare Master Mix + Sample Dilution",null,null,null,"30 min"]
[null,3.2,"Load GEM-X FX Chip",null,null,null,"10 min"]
[null,3.3,"Run the Chromium X/iX",null,null,null,"6 min"]
[null,3.4,"Transfer Gel Beads-in-Emulsion (GEMs)",null,null,null,"5 min"]
[null,3.5,"GEM Incubation",null,null,null,"125 min",null,"4°C ≤1 week (GEMs) or -80°C ≤12 months (washed undiluted sample from step 2.1)"]
[null,"Step 4: GEM Recovery and Pre-Amplification"]
[null,4.0999999999999996,"Post-GEM Incubation – Recovery",null,null,null,"10 min"]
[null,4.2,"Pre-Amplification PCR",null,null,null,"55 min",null,"4°C ≤72 h/-20°C ≤1 week"]
[null,4.3,"DNA Cleanup – SPRIselect",null,null,null,"30 min",null,"4°C ≤72 h/-20°C ≤4 weeks"]
[null,"Step 5: GEM-X Flex – Gene Expression Library Construction"]
[null,5.2,"Sample Index PCR",null,null,null,"40–60 min**",null,"4°C ≤72 h"]
[null,5.3,"Post Sample Index PCR Size Selection – SPRIselect",null,null,null,"30 min",null,"4°C ≤72 h/-20°C long term"]
[null,5.4,"Post Library Construction QC",null,null,null,"60 min"]
[null,"Step 6: GEM-X Flex – Protein Expression Library Construction***"]
[null,6.1,"Sample Index PCR",null,null,null,"40–60 min**",null,"4°C ≤72 h"]
[null,6.2,"Post Sample Index PCR Size Selection – SPRIselect",null,null,null,"30 min",null,"4°C ≤72 h/-20°C long term"]
[null,6.3,"Post Library Construction QC",null,null,null,"60 min"]
[null,"*Pooling is only applicable to multiplexing workflows"]
[null,"**Variable depending upon the cycle number determination method used. See relevant User Guides for details."]
[null,"***Only applicable to gene and protein expression workflows (CG000788 and CG000789)"]
[]
[]
["Data Analysis Overview"]
[" For Gene Expression Only (Workflows 1 & 2)"]
[]
[]
[]
["For Gene & Protein Expression (Workflows 3 & 4)"]
[]
[]
[]
[null,"The following key information should be collected and provided to the data analyst/bioinformatician to ensure that the parameters are set appropriately for Cell Ranger to analyze the data:"]
[null," •","Target number of cells to be recovered per sample"]
[null," •","Sample and library name to be appended to the FASTQ file name and the corresponding library type"]
[null," •","The sample indices used for each GEM-X Flex – Gene Expression, Protein Expression, or CRISPR Guide Capture\nlibrary"]
[null," •","The probe set used (human, mouse, custom)"]
[null," •","The Probe Barcodes used for each sample in a multiplexing experiment"]
[null," •","The Probe Barcodes and Antibody/CRISPR Multiplexing Barcodes used for each sample in a multiplexing experiment "]
[null," •","For Protein libraries, the antibody barcode sequence associated with each feature (for the Feature Reference\nCSV file)"]
[null," •","For CRISPR Guide Capture libraries, CRISPR barcode sequence associated with each feature (for the Feature Reference CSV file)"]
[]
["Document Revision Summary"]
[null,"Updated","Version","Summary of Changes"]
[null,"10/2024","Rev A","Document creation"]
[]
[]
[null,"© 2024 10x Genomics, Inc. (10x Genomics). All rights reserved. Duplication and/or reproduction of all or any portion of this document without the express written consent of 10x Genomics, is strictly forbidden.  Nothing contained herein shall constitute any warranty, express or implied, as to the performance of any products described herein. Any and all warranties applicable to any products are set forth in the applicable terms and conditions of sale accompanying the purchase of such product. 10x Genomics provides no warranty and hereby disclaims any and all warranties as to the use of any third-party products or protocols described herein. The use of products described herein is subject to certain restrictions as set forth in the applicable terms and conditions of sale accompanying the purchase of such product. A non-exhaustive list of 10x Genomics’ marks, many of which are registered in the United States and other countries can be viewed at: www.10xgenomics.com/trademarks. 10x Genomics may refer to the products or services offered by other companies by their brand name or company name solely for clarity, and does not claim any rights in those third-party marks or names. 10x Genomics products may be covered by one or more of the patents as indicated at: www.10xgenomics.com/patents. All products and services described herein are intended FOR RESEARCH USE ONLY and NOT FOR USE IN DIAGNOSTIC PROCEDURES. \n\nThe use of 10x Genomics products in practicing the methods set forth herein has not been validated by 10x Genomics, and such non-validated use is NOT COVERED BY \n10X GENOMICS STANDARD WARRANTY, AND 10X GENOMICS HEREBY DISCLAIMS ANY AND ALL WARRANTIES FOR SUCH USE. Nothing in this document should be construed \nas altering, waiving or amending in any manner 10x Genomics terms and conditions of sale for the Chromium Controller or the Chromium Single Cell Controller, consumables or software, including without limitation such terms and conditions relating to certain use restrictions, limited license, warranty and limitation of liability, and nothing in this document shall be deemed to be Documentation, as that term is set forth in such terms and conditions of sale. Nothing in this document shall be construed as any representation by 10x Genomics that it currently or will at any time in the future offer or in any way support any application set forth herein."]
[]
["Contact"]
[null,"support@10xgenomics.com"]
[null,"10x Genomics"]
[null,"6230 Stoneridge Mall Road"]
[null,"Pleasanton, CA 94588 USA"]

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[null,"PROTOCOL PLANNER  |  CG000780  Rev A  |  10xgenomics.com"]
[null,"GEM-X Flex Gene Expression"]
[]
["Recommended Thermocyclers"]
[null,"The table below lists the thermal cyclers that have been validated by 10x Genomics for all currently available Chromium Single Cell protocols."]
[]
[null,"Description",null,null,null,null,"Supplier",null,"Part Number (US)"]
[null,"Biometra TAdvanced 96 SG/S",null,null,null,null,"Analytik Jena*",null,"846-x-070-241/846-x-070-251\n(x = 2 for 230 V; 4 for 115 V; 5 for 100 V, 50-60 Hz)"]
[null,"Mastercycler X50s/X50a",null,null,null,null,"Eppendorf**",null,"6311000010/6313000018"]
[null,"VeritiPro Thermal Cycler, 96-well",null,null,null,null,"Thermo Fisher Scientific*** ",null,"A48141"]
[null,"PTC Tempo Deepwell Thermal Cycler ",null,null,null,null,"Bio-Rad",null,12015392]
[null,"C1000 Touch Thermal Cycler with 96-Deep Well Reaction Module (discontinued)",null,null,null,null,"Bio-Rad",null,1851197]
[null,"For select instruments, ramp rates should be adjusted for all steps as described below:\n*Analytik Jena Biometra TAdvanced 96 SG/S: 2°C/sec for both heating and cooling\n**Eppendorf Mastercycler X50s/X50a: 3°C/sec heating and 2°C/sec cooling                                                                                                ***Thermo Fisher VeritiPro requires FW 1.2.0, 96 well tray/retainer (PN 4381850), and “Cover Ramping” enabled"]
[]
["Recommended Real Time qPCR Systems"]
["For Optional Gene & Protein Expression Library - Cycle Number Determination Using qPCR "]
[null,"Description",null,null,null,null,"Supplier",null,"Part Number (US)"]
[null,"QuantStudio 12K Flex System",null,null,null,null,"Applied Biosystems",null,4471087]
[null,"CFX96 Real-time System (discontinued)",null,null,null,null,"Bio-Rad",null,1855096]

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[null,"PROTOCOL PLANNER  |  CG000780  Rev A  |  10xgenomics.com"]
[null,"GEM-X Flex Gene Expression"]
[]
["Recommended Pipette Tips "]
[null,"10x Genomics recommends using only validated emulsion-safe pipette tips for all Single Cell protocols. Rainin pipette tips have been extensively validated by 10x Genomics and are highly recommended for all single cell assays. If Rainin tips are unavailable, any of the listed alternate pipette tips validated by 10x Genomics may be used."]
[null,"Supplier",null,"Description",null,null,null,null,null,"Part Number (US)"]
[null,"Pipettes"]
[null,"Rainin",null,"Pipet-Lite Multi Pipette L8-50XLS+",null,null,null,null,null,17013804]
[null,null,null,"Pipet-Lite Multi Pipette L8-200XLS+",null,null,null,null,null,17013805]
[null,null,null,"Pipet-Lite Multi Pipette L8-10XLS+",null,null,null,null,null,17013802]
[null,null,null,"Pipet-Lite Multi Pipette L8-20XLS+",null,null,null,null,null,17013803]
[null,null,null,"Pipet-Lite LTS Pipette L-2XLS+",null,null,null,null,null,17014393]
[null,null,null,"Pipet-Lite LTS Pipette L-10XLS+",null,null,null,null,null,17014388]
[null,null,null,"Pipet-Lite LTS Pipette L-20XLS+",null,null,null,null,null,17014392]
[null,null,null,"Pipet-Lite LTS Pipette L-100XLS+",null,null,null,null,null,17014384]
[null,null,null,"Pipet-Lite LTS Pipette L-200XLS+",null,null,null,null,null,17014391]
[null,null,null,"Pipet-Lite LTS Pipette L-1000XLS+",null,null,null,null,null,17014382]
[null,"Pipette Tips"]
[null,"Rainin",null,"Tips LTS 200UL Filter RT-L200FLR",null,null,null,null,null,30389240]
[null,null,null,"Tips LTS 1ML Filter RT-L1000FLR",null,null,null,null,null,30389213]
[null,null,null,"Tips LTS 20UL Filter RT-L10FLR",null,null,null,null,null,30389226]
[null,"Alternate Recommendations  (If Rainin pipette tips are unavailable, any of the listed pipette tips may be used)"]
[null,"Pipettes"]
[null,"Eppendorf",null,"Eppendorf Research plus, 8-channel, epT.I.P.S. Box, 0.5 – 10 µL",null,null,null,null,null,3125000010]
[null,null,null,"Eppendorf Research plus, 8-channel, epT.I.P.S. Box, 10 – 100 µL",null,null,null,null,null,3125000036]
[null,null,null,"Eppendorf Research plus, 8-channel, epT.I.P.S. Box, 30 – 300 µL",null,null,null,null,null,3125000052]
[null,null,null,"Eppendorf Research plus, 1-channel, epT.I.P.S.® Box, 0.1 – 2.5 µL",null,null,null,null,null,3123000012]
[null,null,null,"Eppendorf Research plus, 1-channel, epT.I.P.S.® Box, 0.5 – 10 µL",null,null,null,null,null,3123000020]
[null,null,null,"Eppendorf Research plus, 1-channel, epT.I.P.S.® Box, 2 – 20 µL",null,null,null,null,null,3123000039]
[null,null,null,"Eppendorf Research plus, 1-channel, epT.I.P.S.® Box, 2 – 200 µL",null,null,null,null,null,3123000055]
[null,null,null,"Eppendorf Research plus, 1-channel, epT.I.P.S.® Box, 100 – 1000 µL",null,null,null,null,null,3123000063]
[null,"Pipette Tips (compatible with Eppendorf pipettes only)"]
[null,"Eppendorf",null,"ep Dualfilter T.I.P.S., 2-20 µL",null,null,null,null,null,30078535]
[null,null,null,"ep Dualfilter T.I.P.S., 2-200 µL",null,null,null,null,null,30078551]
[null,null,null,"ep Dualfilter T.I.P.S., 2-1,000 µL",null,null,null,null,null,30078578]
[null,"Pipette Tips (Compatible with Rainin pipettes)"]
[null,"Labcon",null,"ZAP SLIK 20 µL Low Retention Aerosol Filter Pipet Tips for Rainin LTS",null,null,null,null,null,"4-1143-965-008"]
[null,null,null,"ZAP SLIK 200 µL Low Retention Aerosol Filter Pipet Tips for Rainin LTS",null,null,null,null,null,"4-1144-965-008"]
[null,null,null,"ZAP SLIK 1200 µL Low Retention Aerosol Filter Pipet Tips for Rainin LTS",null,null,null,null,null,"4-1145-965-008"]
[null,"Pipettes Tips (Compatible with Rainin pipettes)"]
[null,"Biotix",null,"xTIP4  Racked Pipette Tips, Rainin LTS Pipette Compatible, 0.1-20uL ",null,null,null,null,null,63300931]
[null,null,null,"xTIP4  Racked Pipette Tips, Rainin LTS Pipette Compatible, 200uL ",null,null,null,null,null,63300001]
[null,null,null,"xTIP4  Racked Pipette Tips, Rainin LTS Pipette Compatible, 1200uL",null,null,null,null,null,63300004]

{"sheet":"Library Constr. ","index":3,"n_rows":69,"n_cols":10,"rows_kept":69,"cut":false,"hidden":false,"merged":[[8,1,8,2],[8,3,8,6],[8,7,8,8],[8,9,8,10],[10,0,13,0],[10,1,10,2],[10,3,10,5],[10,7,10,8],[10,9,10,10],[12,7,12,8],[12,9,12,10],[13,1,13,10],[9,1,9,10],[11,3,11,5],[11,7,11,8],[0,1,0,10],[1,1,1,10],[2,0,2,11],[3,0,3,11],[4,0,4,10],[5,1,5,10],[47,3,47,6],[47,9,47,10],[37,7,37,8],[37,9,37,10],[33,3,33,6],[43,1,43,10],[11,9,11,10],[12,3,12,5],[30,1,30,2],[30,3,30,6],[30,7,30,8],[30,9,30,10],[29,3,29,6],[29,7,29,8],[29,9,29,10],[25,1,25,2],[22,1,22,2],[22,3,22,6],[68,1,68,10],[45,1,45,2],[45,3,45,6],[45,7,45,8],[45,9,45,10],[48,3,48,6],[48,7,48,8],[48,9,48,10],[48,1,49,2],[52,1,52,10],[57,3,57,6],[57,7,57,8],[46,1,46,2],[46,3,46,6],[46,7,46,8],[47,7,47,8],[53,1,54,2],[51,3,51,6],[49,3,49,6],[49,7,49,8],[49,9,49,10],[59,9,59,10],[19,9,19,10],[56,7,56,8],[56,9,56,10],[39,7,39,8],[39,9,39,10],[59,7,59,8],[22,7,22,8],[22,9,22,10],[21,1,21,10],[18,1,19,2],[18,3,18,5],[18,7,18,8],[18,9,18,10],[19,3,19,6],[19,7,19,8],[23,1,23,2],[23,3,23,6],[23,7,23,8],[23,9,23,10],[24,1,24,2],[24,3,24,6],[24,7,24,8],[38,7,38,8],[38,9,38,10],[31,1,31,2],[31,3,31,6],[31,7,31,8],[31,9,31,10],[24,9,24,10],[26,3,26,6],[26,7,26,8],[26,9,26,10],[27,3,27,6],[27,7,27,8],[26,1,27,2],[27,9,27,10],[25,7,25,8],[25,9,25,10],[25,3,25,6],[14,7,14,8],[14,9,14,10],[15,1,15,2],[15,3,15,6],[15,7,15,8],[15,9,15,10],[17,1,17,2],[17,3,17,6],[17,7,17,8],[17,9,17,10],[16,1,16,2],[16,3,16,6],[16,7,16,8],[16,9,16,10],[14,1,14,2],[14,3,14,6],[46,12,57,16],[67,1,67,6],[64,1,64,10],[65,7,65,8],[65,9,65,10],[63,1,63,2],[63,3,63,6],[63,7,63,8],[63,9,63,10],[66,1,66,2],[66,3,66,6],[67,7,67,8],[67,9,67,10],[57,9,57,10],[58,3,58,6],[58,7,58,8],[58,9,58,10],[46,9,46,10],[47,1,47,2],[62,1,62,10],[59,3,59,6],[61,3,61,6],[60,3,60,6],[59,1,61,2],[29,1,29,2],[28,1,28,10],[39,3,39,5],[44,1,44,10],[40,3,40,6],[32,1,32,2],[32,3,32,6],[32,7,32,10],[40,7,40,8],[40,9,40,10],[38,3,38,6],[33,7,33,8],[33,9,33,10],[37,3,37,6],[34,9,34,10],[35,9,35,10],[38,1,42,2],[42,3,42,5],[42,7,42,8],[60,7,60,8],[61,7,61,8],[50,3,50,6],[50,7,50,8],[50,9,50,10],[61,9,61,10],[55,1,56,2],[57,1,58,2],[50,1,51,2],[56,3,56,6],[60,9,60,10],[51,7,51,8],[51,9,51,10],[6,1,6,10],[69,1,69,10],[20,1,20,10],[33,1,37,2],[34,3,34,6],[34,7,34,8],[36,7,36,8],[36,9,36,10],[36,3,36,6],[35,3,35,6],[35,7,35,8],[66,7,66,8],[66,9,66,10],[65,1,65,2],[65,3,65,6],[53,3,53,6],[53,7,53,8],[53,9,53,10],[54,3,54,6],[54,7,54,8],[54,9,54,10],[55,3,55,6],[55,7,55,8],[55,9,55,10]]}
[null,"PROTOCOL PLANNER  |  CG000780  Rev A  |  10xgenomics.com"]
[null,"GEM-X Flex Gene Expression"]
[]
["Kits, Reagents & Equipment"]
["For Library Construction (User Guides – CG000786, CG000787, CG000788, & CG000789)"]
[null,"The items in the tables below have been tested by 10x Genomics and perform optimally with the GEM-X Flex Gene Expression protocols. Substituting materials may adversely affect system performance. This list may not include standard laboratory equipment such as water baths, centrifuges, pH meters, freezers etc."]
[null,"The kits, reagents, and equipment required for sample preparation for GEM-X Flex assay are not included in this document. See appropriate Demonstrated Protocol on 10x Genomics support website for items required for sample preparation."]
[]
[null,"Item",null,"Description",null,null,null,"Supplier",null,"Part Number (US)"]
[null,"Plastics"]
[null,"0.2 ml PCR 8-tube strips",null,"PCR Tubes 0.2 ml 8-tube strips",null,null,null,"Eppendorf",null,951010022]
[null,null,null,"TempAssure PCR 8-tube strip",null,null,null,"USA Scientific",null,"1402-4700"]
[null,null,null,"MicroAmp 8-Tube Strip, 0.2 ml\nMicroAmp 8 -Cap Strip, clear",null,null,null,"Thermo Fisher Scientific\nThermo Fisher Scientific",null,"N8010580\nN8010535"]
[null,"(Choose either Eppendorf, USA Scientific or Thermo Fisher Scientific PCR 8-tube strips)"]
[null,"1.5-ml tubes",null,"DNA LoBind Tubes 1.5 ml",null,null,null,"Eppendorf",null,22431021]
[null,"5-ml tubes",null,"DNA LoBind Tubes 5.0 ml",null,null,null,"Eppendorf",null,30108310]
[null,"Centrifuge tubes",null,"Corning Centrifuge Tubes with CentriStar Cap (15 ml), sterile",null,null,null,"Corning",null,430790]
[null,"Centrifuge tubes",null,"Self-Standing Polypropylene Centrifuge Tubes (50 ml), sterile",null,null,null,"Corning",null,430921]
[null,"Filters",null,"Sterile Single-Pack CellTrics Filters",null,null,null,"Sysmex",null,"04-004-2326"]
[null,null,null,"Pre-Separation Filters (30 μm)",null,null,null,"Miltenyi Biotec",null,"130-041-407"]
[null,"(Choose either Sysmex or Miltenyi Biotec filter)"]
[null,"Kits & Reagents"]
[null,"Nuclease-free water",null,"Molecular Grade Nuclease-free Water",null,null,null,"Thermo Fisher Scientific",null,"AM9937"]
[null,"Tween",null,"Tween 20 Surfact-Amps Detergent Solution (10% solution)",null,null,null,"Thermo Fisher Scientific",null,28320]
[null,"SPRI",null,"SPRIselect Reagent Kit",null,null,null,"Beckman Coulter",null,"B23318"]
[null,"Ethanol",null,"Ethyl Alcohol, 200 Proof, anhydrous",null,null,null,"Millipore Sigma",null,"E7023"]
[null,"Glycerol for storage",null,"Glycerol, 99.5%, for molecular biology, DNAse, RNAse and Protease free Alternative to Millipore Sigma product",null,null,null,"Acros Organics",null,327255000]
[null,null,null,"Glycerol for molecular biology, ≥99.0% Alternative to Acros Organics product",null,null,null,"Millipore Sigma",null,"G5516-100ML"]
[null,"(Choose either Acros organic or Millipore Sigma) "]
[null,"Glycerol for loading\nunused wells",null,"Glycerin (glycerol), 50% (v/v) Aqueous Solution",null,null,null,"Ricca Chemical Company",null,"3290-32"]
[null,"Sterile 1X PBS",null,"Phosphate-Buffered Saline without Calcium & Magnesium\nOr any equivalent sterile PBS",null,null,null,"Corning",null,"21-040-CM"]
[null,"Buffer EB",null,"Qiagen Buffer EB",null,null,null,"Qiagen",null,19086]
[null,"For Cell Counting"]
[null,"Cell counter & slides",null,"Countess II FL Automated Cell Counter \nDiscontinued\nRequires additional fluorescent filters\n",null,null,null,"Thermo Fisher Scientific\n",null,"AMQAF1000\n"]
[null,null,null,"Countess 3 FL Automated Cell Counter \n",null,null,null,"Thermo Fisher Scientific\n",null,"A49866\n"]
[null,null,null,"Countess Cell Counting Chamber Slides",null,null,null,"Thermo Fisher Scientific",null,"C10228"]
[null,null,null,"Cellometer K2  Bundle w/ Matrix Software",null,null,null,"Nexcelom Bioscience",null,"CMT-K2-MX-150"]
[null,null,null,"Celleca MX HIgh-throughput Automated Cell Counter",null,null,null,"Nexcelom Bioscience",null,"MX-112-0127"]
[null,"Staining solution",null,"ViaStain AOPI Staining Solution",null,null,null,"Nexcelom Bioscience",null,"CS2-0106-5mL"]
[null,null,null,"ViaStain PI Staining Solution",null,null,null,"Nexcelom Bioscience",null,"CS1-0109-5mL"]
[null,null,null,"Trypan Blue Stain (0.4%)",null,null,null,"Thermo Fisher Scientific",null,"T10282"]
[null,null,null,"NucSpot 470",null,null,null,"Biotium",null,40083]
[null,null,null,"DAPI solution, 1 mg/mL",null,null,null,"Thermo Fisher Scientific",null,62248]
[null,"(Choose either AOPI, NucSpot, PI, or DAPI solution. If the sample has no debris, Trypan Blue can be used.)"]
[null,"Equipment"]
[null,"Centrifuge",null,"Mini Centrifuge\nOr any equivalent mini centrifuge",null,null,null,"VWR",null,"76269-064"]
[null,"Vortex",null,"Vortex Mixer",null,null,null,"VWR",null,"10153-838"]
[null,"Reagent reservoirs",null,"Divided Polystyrene Reservoirs",null,null,null,"VWR",null,"41428-958"]
[null,"Thermomixer",null,"Eppendorf ThermoMixer C",null,null,null,"Eppendorf",null,5382000023]
[null,null,null,"Eppendorf ThermoTop with condens.protect technology \nRequired for overnight hybridization step when using 1.5-ml microcentrifuge tubes",null,null,null,"Eppendorf",null,5308000003]
[null,"Heat block",null,"Eppendorf SmartBlock 1.5 ml, Thermoblock for 24 reaction vessel ",null,null,null,"Eppendorf",null,5360000038]
[null,null,null,"Eppendorf SmartBlock 2.0 ml, Thermoblock for 24 reaction vessels\nOr any equivalent temperature controlled heat block",null,null,null,"Eppendorf",null,5362000035]
[null,"Quantification & Quality Control"]
[null,"Bioanalyzer",null,"2100 Bioanalyzer Laptop Bundle\ndiscontinued",null,null,null,"Agilent",null,"G2953CA"]
[null,null,null,"4200 TapeStation",null,null,null,"Agilent",null,"G2991AA"]
[null,"TapeStation",null,"High Sensitivity D5000: ScreenTape/Reagents",null,null,null,"Agilent",null,"5067-5592 / 5067-5593"]
[null,null,null,"High Sensitivity D1000: ScreenTape/Reagents",null,null,null,"Agilent",null,"5067-5584 / 5067-5585"]
[null,"LabChip\n",null,"LabChip GX Touch HT Nucleic Acid Analyzer",null,null,null,"Revvity",null,"CLS137031"]
[null,null,null,"DNA High Sensitivity Reagent Kit",null,null,null,"PerkinElmer",null,"CLS760672"]
[null,"Fragment analyzer",null,"Fragment Analyzer Automated CE System - 12 cap ",null,null,null,"Advanced Analytical",null,"FSv2-CE2F"]
[null,null,null,"Fragment Analyzer Automated CE System - 48/96 cap ",null,null,null,"Advanced Analytical",null,"FSv2-CE10F"]
[null,null,null,"High Sensitivity NGS Fragment Analysis Kit",null,null,null,"Advanced Analytical",null,"DNF-474"]
[null,"(Choose Bioanalyzer, TapeStation, LabChip, or Fragment Analyzer based on availability & preference.)"]
[null,"Library quantification",null,"KAPA Library Quantification Kit for Illumina Platforms",null,null,null,"KAPA Biosystems",null,"KK4824"]
[null,"Optional Gene & Protein Expression Library - Cycle Number Determination Using qPCR"]
[null,"qPCR Dye",null,"EvaGreen, EvaGreenPlus ",null,null,null,"Biotium",null," 31000-T or 31077-T"]
[null,"Primers for cycle number determination for Protein Expression Libraries*",null,"Forward Primer\nCTACACGACGCTCTTCCGATCT\nReverse Primer\nCTCGTGGGCTCGGAGATGTGTATAAGAGACAG",null,null,null,"_",null,"_"]
[null,"*Only needed for GEM-X Flex Protein Expression libraries"]
[null,"For some items, a number of vendor options are listed. Choose item based on availability and preference. Refer to the manufacturer's website for regional part numbers. "]

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