Journal: bioRxiv

Article Title: Automation workflow for high-throughput arrayed plasmid DNA preparation and quantification

doi: 10.64898/2025.12.13.694144

Figure Lengend Snippet: A. Hardware layout of the Biomek i7 Hybrid automated workstation. B. Schematic overview of arrayed bacterial inoculation. ① Four empty 96-deep-well plates were initially placed on the Biomek deck. ② 1.2 mL of terrific broth (TB) were transferred from reservoirs to the 96-deep-well plates using the 96-channel pipette head. ③ Four 96-well round-bottom plates containing freshly thawed bacteria glycerol stocks were transferred to the Biomek i7 deck via the servo shuttle and track gripper. The lids were removed and placed on the deck by the gripper. ④ 50 µL of bacteria glycerol solution was transferred from the round-bottom plates to the deep-well plates and mixed thoroughly using the 96-channel pipette head. ⑤ The lids were replaced, and the plates containing leftover bacterial glycerol stocks were returned to the incubator. C. Pipeline overview under the SAMI EX interface. SAMI EX software was utilized for the method creation and pipeline design. D. SAMI’s scheduling and time estimation for the pipeline illustrated the chronological timestamps of each labware. E. The labware setup report provided a reference point and summarizes the SAMI EX deck layout, labware, and associated conditions.

Article Snippet: The automation workflow for high throughput arrayed plasmid DNA preparation and quantification on the Biomek i7 platform was established using the Beckman Coulter software suite.

Techniques: Transferring, Bacteria, Software

Journal: bioRxiv

Article Title: Automation workflow for high-throughput arrayed plasmid DNA preparation and quantification

doi: 10.64898/2025.12.13.694144

Figure Lengend Snippet: A. Schematic overview of arrayed plasmid isolation using Biomek i7 liquid handler and BioShake. ① RES buffer was transferred from a reservoir to a 96-deep-well plate containing dry bacterial pellets on the Biomek deck. ② The plate was moved to the shaker by the gripper for vortexing, followed by pipetting up and down using the 96-channel pipette head to fully resuspend the bacteria. ③ LYS buffer was then transferred from a reservoir to the plate, followed by pipetting up and down to ensure complete bacterial lysis. ④ NEU buffer was added from a reservoir to the plate, followed by pipetting up and down to neutralize the alkaline lysate. Biomek 5 method node: asterisk symbol; SAMI EX method node: black dot symbol. B. Pipeline overview under the SAMI EX interface. Both SAMI EX and Biomek 5 software were utilized for the method development. C. Scheduling and time estimation of the entire pipeline in SAMI EX, showing the chronological timestamps of each labware item. D. Deck layout for RES buffer transfer and plate vortexing, indicated by the asterisk in . E. Biomek 5 method for RES buffer transfer and plate vortexing (asterisk in ). F. Labware setup report, indicated by the dagger symbol in , providing an overview of the SAMI EX deck layout, including labware details and conditions.

Article Snippet: The automation workflow for high throughput arrayed plasmid DNA preparation and quantification on the Biomek i7 platform was established using the Beckman Coulter software suite.

Techniques: Plasmid Preparation, Isolation, Transferring, Bacteria, Lysis, Software

Journal: bioRxiv

Article Title: Automation workflow for high-throughput arrayed plasmid DNA preparation and quantification

doi: 10.64898/2025.12.13.694144

Figure Lengend Snippet: A. Schematic overview of arrayed plasmid DNA purification using the Biomek i7 liquid handler, BioShake, microplate centrifuge, and magnetic plate. All steps (① - ⑬) were performed within the Biomek i7 system. ① Molecular-grade water was added to the 96-deep-well plate containing dry DNA pellets. ② The plate was transferred to the BioShake for vortexing.③ The plate was transferred to the centrifuge to spin down DNA suspension. ④ The plate was returned to the BioShake and remained there for the next two steps. ⑤ Bead buffer was added to the plate, and then vortexed. ⑥ Bead solution was added to the plate, followed by vortexing and incubation to enable DNA-bead binding. ⑦ The plate was transferred to the centrifuge for a brief spin-down. ⑧ The plate was placed on the magnetic plate for DNA-bead isolation and remained there for the subsequent steps, except step 10. ⑨ After liquid removal by pipetting, 70% ethanol (ETOH) was added to the plate for DNA washing, followed by liquid removal and a repeat wash. ⑩ After removing the second wash, the plate was transferred from the magnetic plate to the pre-warmed BioShake. ⑪ TE buffer was added to the plate, followed by vortexing and incubation on the BioShake for DNA elution. ⑫ The plate was then placed back onto the magnetic plate for DNA-bead separation. ⑬ The supernatant containing plasmid DNA was transferred to a new 96-well conical-bottom plate, followed by a secondary transfer to another plate to remove any residual beads. B. Pipeline overview displayed in the SAMI EX interface. Method development and pipeline design were performed using the SAMI EX and Biomek 5 software platforms. C. SAMI EX provides scheduling and time estimation for the entire pipeline, displaying the chronological timestamps for each labware item. D. Overview and deck layout of the three Biomek 5 methods: buffer and bead treatment for DNA-bead binding (top-left panel), ethanol wash and TE addition for DNA washing and elution (right panel), and DNA solution clarification through bead removal (bottom-left panel), as indicated by the asterisk in . E. The labware setup report, marked by the dagger symbol in , outlines the SAMI EX deck layout and labware conditions.

Article Snippet: The automation workflow for high throughput arrayed plasmid DNA preparation and quantification on the Biomek i7 platform was established using the Beckman Coulter software suite.

Techniques: Plasmid Preparation, DNA Purification, Suspension, Incubation, Binding Assay, Isolation, Software, Clarification Assay

Journal: bioRxiv

Article Title: Automation workflow for high-throughput arrayed plasmid DNA preparation and quantification

doi: 10.64898/2025.12.13.694144

Figure Lengend Snippet: A. Overview of arrayed plasmid DNA quantification using the Biomek i7 liquid handler and microplate centrifuge. All steps (① - ⑩) were performed within the Biomek i7 system. ① A 96-well plate containing 2 ng/µL standard DNA in well A1 and PicoGreen reagent in columns 2-4 was designated as the reagent plate. TE buffer, stored in a reservoir, was used as the diluent to perform a six-point, three-fold serial dilution from wells A1 to G1 in column 1. The negative control well, H1, contained TE buffer without DNA. ② Twenty microliters of the serially diluted DNA and TE buffer in column 1 were transferred from the reagent plate to the quadruple 1 (Q1) well positions in columns 1, 3, and 5 of a new 384-well assay plate as the standard and negative controls, each in triplicate. ③ TE buffer was transferred from the reservoir to a new 96-well conical-bottom plate (designated as the 1:20 dilution plate) to serve as the diluent for the first DNA sample dilution. ④ TE buffer was also transferred from the reservoir to another 96-well conical-bottom plate (designated as the 1:400 dilution plate) to serve as the diluent for the second dilution. ⑤ Purified plasmid DNA samples in a 96-well plate were transferred to the 1:20 dilution plate to generate an intermediate dilution stock. ⑥ The intermediately diluted DNA was transferred to the 1:400 dilution plate to achieve the final dilution. ⑦ The final diluted DNA samples from the 1:400 dilution plate were transferred to the Q3 and Q4 wells of the assay plate in duplicate. ⑧ PicoGreen reagent was transferred from the reagent plate to the Q1, Q3, and Q4 well positions of the assay plate. ⑨ The assay plate was subjected to a brief spin-down. ⑩ The assay plate was then placed on the BioShake for sample mixing prior to measurement. B. Pipeline overview as displayed in the SAMI EX interface. Method development and pipeline design were carried out using the SAMI EX and Biomek 5 software. C. SAMI EX generated a schedule and time estimate for the entire pipeline, including chronological timestamps for each labware item. D. Overview and deck layout of the four Biomek 5 methods: serial dilution of the standard DNA (top-left panel), spotting of the standard and negative controls (bottom-left panel), dilution of the plasmid DNA samples (top-right panel), and dispensing of the PicoGreen reagent (bottom-right panel), as indicated by the asterisk in . E. The labware setup report, marked by the dagger in , outlines the SAMI EX deck layout and labware conditions.

Article Snippet: The automation workflow for high throughput arrayed plasmid DNA preparation and quantification on the Biomek i7 platform was established using the Beckman Coulter software suite.

Techniques: Plasmid Preparation, Serial Dilution, Negative Control, Purification, Software, Generated

Journal: bioRxiv

Article Title: Automation workflow for high-throughput arrayed plasmid DNA preparation and quantification

doi: 10.64898/2025.12.13.694144

Figure Lengend Snippet: A. Plasmid DNA quantities from five 96-well plates (480 samples from the T. gonfio library), generated using the Biomek i7 and measured by the NanoDrop, are presented as overlapping scatter and box plots. The median value is indicated by a red line, and the green box denotes the interquartile range. The gray solid line marks the high-titer threshold of 10 µg of DNA. B. Comparison of DNA concentration measurements between the NanoDrop and PicoGreen assay across four 96-well plates. The median is shown in red, while the gray solid line represents the 10 µg DNA threshold. C. Scatter plots depicting the correlation (R²) between DNA concentrations measured by the NanoDrop and the PicoGreen assay across four plates. The values on the X- and Y-axes represent individual DNA concentrations measured by the two methods. D. Gel electrophoresis image showing the migration pattern of equal amounts of plasmid DNA (60 ng per lane) after PicoGreen-based concentration normalization, alongside 1 kb DNA ladders. The intensities of the 6 kb and 8 kb ladder bands each represent 2.8 ng of DNA.

Article Snippet: The automation workflow for high throughput arrayed plasmid DNA preparation and quantification on the Biomek i7 platform was established using the Beckman Coulter software suite.

Techniques: Plasmid Preparation, Generated, Comparison, Concentration Assay, Picogreen Assay, Nucleic Acid Electrophoresis, Migration

Journal: bioRxiv

Article Title: Automation workflow for high-throughput arrayed plasmid DNA preparation and quantification

doi: 10.64898/2025.12.13.694144

Figure Lengend Snippet: A. Hardware layout of the Biomek i7 Hybrid automated workstation. B. Schematic overview of arrayed bacterial inoculation. ① Four empty 96-deep-well plates were initially placed on the Biomek deck. ② 1.2 mL of terrific broth (TB) were transferred from reservoirs to the 96-deep-well plates using the 96-channel pipette head. ③ Four 96-well round-bottom plates containing freshly thawed bacteria glycerol stocks were transferred to the Biomek i7 deck via the servo shuttle and track gripper. The lids were removed and placed on the deck by the gripper. ④ 50 µL of bacteria glycerol solution was transferred from the round-bottom plates to the deep-well plates and mixed thoroughly using the 96-channel pipette head. ⑤ The lids were replaced, and the plates containing leftover bacterial glycerol stocks were returned to the incubator. C. Pipeline overview under the SAMI EX interface. SAMI EX software was utilized for the method creation and pipeline design. D. SAMI’s scheduling and time estimation for the pipeline illustrated the chronological timestamps of each labware. E. The labware setup report provided a reference point and summarizes the SAMI EX deck layout, labware, and associated conditions.

Article Snippet: The Biomek i7 automated liquid handling system (Product No. B87585, Beckman Coulter) is equipped with hybrid multichannel pods, a dual-pod system combining 96/384-channel heads and eight independent pipette heads, along with a barcode reader, two track grippers, a plate shuttle station, a Biotek 405 LSHTV Washer (Agilent), a BioShake 3000-T ELM microplate shaker (QInstruments), a Cytomat 2C hotel incubator (Thermo Fisher Scientific), a CloneSelect imager (Molecular Devices), and a microcentrifuge (Agilent).

Techniques: Transferring, Bacteria, Software

Journal: bioRxiv

Article Title: Automation workflow for high-throughput arrayed plasmid DNA preparation and quantification

doi: 10.64898/2025.12.13.694144

Figure Lengend Snippet: A. Schematic overview of arrayed plasmid isolation using Biomek i7 liquid handler and BioShake. ① RES buffer was transferred from a reservoir to a 96-deep-well plate containing dry bacterial pellets on the Biomek deck. ② The plate was moved to the shaker by the gripper for vortexing, followed by pipetting up and down using the 96-channel pipette head to fully resuspend the bacteria. ③ LYS buffer was then transferred from a reservoir to the plate, followed by pipetting up and down to ensure complete bacterial lysis. ④ NEU buffer was added from a reservoir to the plate, followed by pipetting up and down to neutralize the alkaline lysate. Biomek 5 method node: asterisk symbol; SAMI EX method node: black dot symbol. B. Pipeline overview under the SAMI EX interface. Both SAMI EX and Biomek 5 software were utilized for the method development. C. Scheduling and time estimation of the entire pipeline in SAMI EX, showing the chronological timestamps of each labware item. D. Deck layout for RES buffer transfer and plate vortexing, indicated by the asterisk in . E. Biomek 5 method for RES buffer transfer and plate vortexing (asterisk in ). F. Labware setup report, indicated by the dagger symbol in , providing an overview of the SAMI EX deck layout, including labware details and conditions.

Article Snippet: The Biomek i7 automated liquid handling system (Product No. B87585, Beckman Coulter) is equipped with hybrid multichannel pods, a dual-pod system combining 96/384-channel heads and eight independent pipette heads, along with a barcode reader, two track grippers, a plate shuttle station, a Biotek 405 LSHTV Washer (Agilent), a BioShake 3000-T ELM microplate shaker (QInstruments), a Cytomat 2C hotel incubator (Thermo Fisher Scientific), a CloneSelect imager (Molecular Devices), and a microcentrifuge (Agilent).

Techniques: Plasmid Preparation, Isolation, Transferring, Bacteria, Lysis, Software

Journal: bioRxiv

Article Title: Automation workflow for high-throughput arrayed plasmid DNA preparation and quantification

doi: 10.64898/2025.12.13.694144

Figure Lengend Snippet: A. Schematic overview of arrayed plasmid DNA purification using the Biomek i7 liquid handler, BioShake, microplate centrifuge, and magnetic plate. All steps (① - ⑬) were performed within the Biomek i7 system. ① Molecular-grade water was added to the 96-deep-well plate containing dry DNA pellets. ② The plate was transferred to the BioShake for vortexing.③ The plate was transferred to the centrifuge to spin down DNA suspension. ④ The plate was returned to the BioShake and remained there for the next two steps. ⑤ Bead buffer was added to the plate, and then vortexed. ⑥ Bead solution was added to the plate, followed by vortexing and incubation to enable DNA-bead binding. ⑦ The plate was transferred to the centrifuge for a brief spin-down. ⑧ The plate was placed on the magnetic plate for DNA-bead isolation and remained there for the subsequent steps, except step 10. ⑨ After liquid removal by pipetting, 70% ethanol (ETOH) was added to the plate for DNA washing, followed by liquid removal and a repeat wash. ⑩ After removing the second wash, the plate was transferred from the magnetic plate to the pre-warmed BioShake. ⑪ TE buffer was added to the plate, followed by vortexing and incubation on the BioShake for DNA elution. ⑫ The plate was then placed back onto the magnetic plate for DNA-bead separation. ⑬ The supernatant containing plasmid DNA was transferred to a new 96-well conical-bottom plate, followed by a secondary transfer to another plate to remove any residual beads. B. Pipeline overview displayed in the SAMI EX interface. Method development and pipeline design were performed using the SAMI EX and Biomek 5 software platforms. C. SAMI EX provides scheduling and time estimation for the entire pipeline, displaying the chronological timestamps for each labware item. D. Overview and deck layout of the three Biomek 5 methods: buffer and bead treatment for DNA-bead binding (top-left panel), ethanol wash and TE addition for DNA washing and elution (right panel), and DNA solution clarification through bead removal (bottom-left panel), as indicated by the asterisk in . E. The labware setup report, marked by the dagger symbol in , outlines the SAMI EX deck layout and labware conditions.

Article Snippet: The Biomek i7 automated liquid handling system (Product No. B87585, Beckman Coulter) is equipped with hybrid multichannel pods, a dual-pod system combining 96/384-channel heads and eight independent pipette heads, along with a barcode reader, two track grippers, a plate shuttle station, a Biotek 405 LSHTV Washer (Agilent), a BioShake 3000-T ELM microplate shaker (QInstruments), a Cytomat 2C hotel incubator (Thermo Fisher Scientific), a CloneSelect imager (Molecular Devices), and a microcentrifuge (Agilent).

Techniques: Plasmid Preparation, DNA Purification, Suspension, Incubation, Binding Assay, Isolation, Software, Clarification Assay

Journal: bioRxiv

Article Title: Automation workflow for high-throughput arrayed plasmid DNA preparation and quantification

doi: 10.64898/2025.12.13.694144

Figure Lengend Snippet: A. Overview of arrayed plasmid DNA quantification using the Biomek i7 liquid handler and microplate centrifuge. All steps (① - ⑩) were performed within the Biomek i7 system. ① A 96-well plate containing 2 ng/µL standard DNA in well A1 and PicoGreen reagent in columns 2-4 was designated as the reagent plate. TE buffer, stored in a reservoir, was used as the diluent to perform a six-point, three-fold serial dilution from wells A1 to G1 in column 1. The negative control well, H1, contained TE buffer without DNA. ② Twenty microliters of the serially diluted DNA and TE buffer in column 1 were transferred from the reagent plate to the quadruple 1 (Q1) well positions in columns 1, 3, and 5 of a new 384-well assay plate as the standard and negative controls, each in triplicate. ③ TE buffer was transferred from the reservoir to a new 96-well conical-bottom plate (designated as the 1:20 dilution plate) to serve as the diluent for the first DNA sample dilution. ④ TE buffer was also transferred from the reservoir to another 96-well conical-bottom plate (designated as the 1:400 dilution plate) to serve as the diluent for the second dilution. ⑤ Purified plasmid DNA samples in a 96-well plate were transferred to the 1:20 dilution plate to generate an intermediate dilution stock. ⑥ The intermediately diluted DNA was transferred to the 1:400 dilution plate to achieve the final dilution. ⑦ The final diluted DNA samples from the 1:400 dilution plate were transferred to the Q3 and Q4 wells of the assay plate in duplicate. ⑧ PicoGreen reagent was transferred from the reagent plate to the Q1, Q3, and Q4 well positions of the assay plate. ⑨ The assay plate was subjected to a brief spin-down. ⑩ The assay plate was then placed on the BioShake for sample mixing prior to measurement. B. Pipeline overview as displayed in the SAMI EX interface. Method development and pipeline design were carried out using the SAMI EX and Biomek 5 software. C. SAMI EX generated a schedule and time estimate for the entire pipeline, including chronological timestamps for each labware item. D. Overview and deck layout of the four Biomek 5 methods: serial dilution of the standard DNA (top-left panel), spotting of the standard and negative controls (bottom-left panel), dilution of the plasmid DNA samples (top-right panel), and dispensing of the PicoGreen reagent (bottom-right panel), as indicated by the asterisk in . E. The labware setup report, marked by the dagger in , outlines the SAMI EX deck layout and labware conditions.

Article Snippet: The Biomek i7 automated liquid handling system (Product No. B87585, Beckman Coulter) is equipped with hybrid multichannel pods, a dual-pod system combining 96/384-channel heads and eight independent pipette heads, along with a barcode reader, two track grippers, a plate shuttle station, a Biotek 405 LSHTV Washer (Agilent), a BioShake 3000-T ELM microplate shaker (QInstruments), a Cytomat 2C hotel incubator (Thermo Fisher Scientific), a CloneSelect imager (Molecular Devices), and a microcentrifuge (Agilent).

Techniques: Plasmid Preparation, Serial Dilution, Negative Control, Purification, Software, Generated

Journal: bioRxiv

Article Title: Automation workflow for high-throughput arrayed plasmid DNA preparation and quantification

doi: 10.64898/2025.12.13.694144

Figure Lengend Snippet: A. Plasmid DNA quantities from five 96-well plates (480 samples from the T. gonfio library), generated using the Biomek i7 and measured by the NanoDrop, are presented as overlapping scatter and box plots. The median value is indicated by a red line, and the green box denotes the interquartile range. The gray solid line marks the high-titer threshold of 10 µg of DNA. B. Comparison of DNA concentration measurements between the NanoDrop and PicoGreen assay across four 96-well plates. The median is shown in red, while the gray solid line represents the 10 µg DNA threshold. C. Scatter plots depicting the correlation (R²) between DNA concentrations measured by the NanoDrop and the PicoGreen assay across four plates. The values on the X- and Y-axes represent individual DNA concentrations measured by the two methods. D. Gel electrophoresis image showing the migration pattern of equal amounts of plasmid DNA (60 ng per lane) after PicoGreen-based concentration normalization, alongside 1 kb DNA ladders. The intensities of the 6 kb and 8 kb ladder bands each represent 2.8 ng of DNA.

Article Snippet: The Biomek i7 automated liquid handling system (Product No. B87585, Beckman Coulter) is equipped with hybrid multichannel pods, a dual-pod system combining 96/384-channel heads and eight independent pipette heads, along with a barcode reader, two track grippers, a plate shuttle station, a Biotek 405 LSHTV Washer (Agilent), a BioShake 3000-T ELM microplate shaker (QInstruments), a Cytomat 2C hotel incubator (Thermo Fisher Scientific), a CloneSelect imager (Molecular Devices), and a microcentrifuge (Agilent).

Techniques: Plasmid Preparation, Generated, Comparison, Concentration Assay, Picogreen Assay, Nucleic Acid Electrophoresis, Migration