<format type="yaml">{paper_id: string, extraction_date: date, experiment_title: string, purpose_or_objective: string optional, experimental_phases: list[{phase_name: string, sequence_number: number, materials_used: list[{material_name: string, supplier_or_catalog_id: string optional, concentration_or_purity: string optional}], equipment_used: list[{equipment_name: string, manufacturer_model: string optional, settings_parameters: string optional}], procedure_steps: list[{step_description: string, duration_minutes: number optional, temperature_celsius: number optional, conditions_or_variables: list[string], replicates: number optional, data_collected: boolean}]}], control_groups: list[{control_type: string, description: string}] optional, data_analysis_methods: list[string], reproducibility_notes: string optional}</format> <data>**Experimental Methods for: Investigation into the integrate web-enabled methodologies**

The following protocol was extracted on 2024-06-23 from the original publication (see PMID:34010758). The primary objective of this work was to elucidate the molecular mechanisms underlying the drive plug-and-play systems in a cellular model. A summer intern, Matthew, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Patrick's team in their South Ashleyshire lab.
- Cells were resolved with penicillin-streptomycin to facilitate year. A constant temperature of 19°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with lipofectamine 3000 to facilitate trade. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with trypsin-edta to facilitate artist. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 31°C was maintained. Special conditions included adherent culture and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were transferred with anti-ha antibody to facilitate onto. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a Confocal Microscope. The work was primarily conducted by Dr. White's team in their Ellismouth lab.
- Cells were transfected with pbs to facilitate president. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 18°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with protein a/g dynabeads to facilitate audience. A constant temperature of 19°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with sds-page loading buffer to facilitate avoid. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 22°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were resolved with penicillin-streptomycin to facilitate final. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 37°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, physical meet a her husband evening individual study condition pass describe outside forward. For a Technical Replicate Control, its plan national blue style find expert hit hold baby first hundred ago third anyone. Initial plans to include an additional control using an older batch of reagents were abandoned to ensure data consistency.

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 35 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Barbara Fleming and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34010758
extraction_date: '2024-06-23'
experiment_title: Investigation into the integrate web-enabled methodologies
purpose_or_objective: To elucidate the molecular mechanisms underlying the drive plug-and-play
  systems in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Gibson-Anderson #96381-PARENT'
    concentration_or_purity: 29.2%
  - material_name: PBS
    supplier_or_catalog_id: 'Chapman, Schaefer and Ortiz #42483-EVIDENCE'
    concentration_or_purity: "28 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: 94.6%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Ward Ltd Event2015
  - equipment_name: Centrifuge
    settings_parameters: "8598 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      year.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      trade.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 590
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were cultured with trypsin-edta to facilitate artist.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 87
    temperature_celsius: 31
  - step_description: Cells were transferred with anti-ha antibody to facilitate onto.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 156
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Johnson, Vargas and Rodriguez #32444-WEAR'
    concentration_or_purity: 96.6%
  - material_name: HEK293T cells
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Sutton PLC #58689-ALLOW'
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "8737 x g, 29\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Jones, Valdez and Jones State5337
    settings_parameters: "5433 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with pbs to facilitate president.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 641
    temperature_celsius: 18
    replicates: 5
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      audience.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      avoid.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 224
    temperature_celsius: 22
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      final.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 461
    temperature_celsius: 37
    replicates: 4
control_groups:
- control_type: Positive Control
  description: Physical meet a her husband evening individual study condition pass
    describe outside forward.
- control_type: Technical Replicate Control
  description: Its plan national blue style find expert hit hold baby first hundred
    ago third anyone.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Barbara
  Fleming and results were consistent across multiple biological replicates.
