epic arrays intact genomic dna yield  (Thermo Fisher)

Journal: STAR Protocols

Article Title: In vivo CRISPR screening protocol to identify metastasis mediators using iteratively selected mouse models

doi: 10.1016/j.xpro.2025.104042

Figure Lengend Snippet: Determining assembly efficiency by gel electrophoresis, related to step 7 sgRNA library insert (∼140 bp), digested pLentiCRISPR_v2 backbone (∼13,000 bp), and HiFi assembly reaction product were resolved on a 2% TAE agarose gel. Electrophoresis was performed at 120 V for 30 min in 1× TAE buffer, followed by SYBR green staining and UV visualization. 1 Kb DNA ladder were included for size validation.

Article Snippet: Synthesize the pooled sgRNA oligo library as a custom DNA array using a commercial high-throughput synthesis service (for instance, GeneWiz or GenScript).

Techniques: Nucleic Acid Electrophoresis, Agarose Gel Electrophoresis, SYBR Green Assay, Staining, Biomarker Discovery

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: Schematic overview of the workflow comprising four automated pipelines and four manual procedures described in Materials and Methods. A. Automated pipelines employed a 96-channel pipette head for liquid handling to perform multiple steps, including inoculating bacteria (Method 2.1 and ) from a glycerol stock plate into a new 96-deep-well plate, dispensing resuspension, lysis, and neutralization buffers for plasmid isolation (Method 4 and ), adding 100% ethanol for DNA precipitation, purifying DNA using magnetic beads with 70% ethanol washes and TE buffer resuspension (Method 6 and ), and diluting plasmid DNA with PicoGreen reagents for fluorescence-based DNA quantification (Method 7 and ). B. Procedures that required manual processing included thawing bacterial plates (Method 2.1), removing and sealing plates, transferring inoculated plates to thermal shakers for 48-hour culture (Method 3), moving plates in and out of the freezer for short- or long-term storage (Method 5), and loading plates into the plate reader for fluorescence analysis (Method 7).

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, Lysis, Neutralization, Plasmid Preparation, Isolation, Magnetic Beads, Fluorescence

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