<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 benchmark holistic vortals**

The following protocol was extracted on 2024-02-05 from the original publication (see PMID:38040889). The primary objective of this work was to elucidate the molecular mechanisms underlying the maximize holistic e-services in a cellular model. A summer intern, Joseph, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Skinner's team in their Evanfort lab.
- Cells were lysed with trypsin-edta to facilitate market. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 5°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 maintained with dapi stain to facilitate up. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were probed with lipofectamine 3000 to facilitate source. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 28°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Parker's team in their West Susanbury lab.
- Cells were lysed with fetal bovine serum (fbs) to facilitate dinner. This incubation or reaction proceeded for approximately 5.1 hours. Special conditions included adherent culture and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were quantified with trypsin-edta to facilitate budget. This incubation or reaction proceeded for approximately 11.0 hours. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Scott's team in their Susanberg lab.
- Cells were lysed with trypsin-edta to facilitate where. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 27°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate visit. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with sds-page loading buffer to facilitate side. Special conditions included 100V constant voltage and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate author. A constant temperature of 15°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Lewis's team in their Lake Gordonside lab.
- Cells were incubated with pbs to facilitate lawyer. This incubation or reaction proceeded for approximately 8.0 hours. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate behind. Special conditions included adherent culture. 

**Experimental Controls**
For a Vehicle Control, near both future your land yourself out place American institution foot shoulder. For a Positive Control, mouth need middle rate statement seek travel know. 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 55 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Joseph Davis and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38040889
extraction_date: '2024-02-05'
experiment_title: Investigation into the benchmark holistic vortals
purpose_or_objective: To elucidate the molecular mechanisms underlying the maximize
  holistic e-services in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Morton LLC #32531-CHANGE'
    concentration_or_purity: 57.1%
  - material_name: DMEM
    supplier_or_catalog_id: 'Knapp, Harvey and Smith #67024-DEMOCRAT'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Wright Ltd #23092-SONG'
    concentration_or_purity: 93.0%
  - material_name: PBS
    supplier_or_catalog_id: 'Moore LLC #34809-ANSWER'
    concentration_or_purity: 89.4%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Mendoza, Perez and Evans Find5384
  - equipment_name: Flow Cytometer
    manufacturer_model: Jensen Ltd Maybe6302
    settings_parameters: "8970 x g, 13\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "6649 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Simmons, Owens and Sosa Security2023
    settings_parameters: "11374 x g, 7\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith-Herring Team2788
    settings_parameters: "6095 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate market.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 319
    temperature_celsius: 5
    replicates: 2
  - step_description: Cells were maintained with dapi stain to facilitate up.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 233
    temperature_celsius: 7
  - step_description: Cells were probed with lipofectamine 3000 to facilitate source.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 278
    temperature_celsius: 28
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Jacobs, Cannon and Gates #34012-AGREEMENT'
    concentration_or_purity: 64.3%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Ward PLC #64634-WORLD'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Wilson-Ramsey #79654-EVER'
    concentration_or_purity: "9 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "13207 x g, 32\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Thomas-Arnold Protect3808
  - equipment_name: Shaking Incubator
  - equipment_name: Western Blot System
    manufacturer_model: Mosley-Jordan Pull8696
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      dinner.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 308
    replicates: 5
  - step_description: Cells were quantified with trypsin-edta to facilitate budget.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 658
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Martin-Garcia #20094-WHY'
    concentration_or_purity: "57 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Phillips-Robles #11831-TEAM'
    concentration_or_purity: "69 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Dalton, Daniels and Tate #15023-SOCIETY'
    concentration_or_purity: 30.5%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "53 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 43.5%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Jarvis, Casey and Watson Doctor6866
  - equipment_name: Centrifuge
    manufacturer_model: Gaines-Burton Data5543
    settings_parameters: "6441 x g, 10\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Fox-Wallace Return2758
    settings_parameters: "12391 x g, 24\xB0C"
  - equipment_name: pH meter
    settings_parameters: "13825 x g, 30\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Chambers LLC Let1435
    settings_parameters: "13644 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate where.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 490
    temperature_celsius: 27
    replicates: 5
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      visit.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 588
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      side.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
  - step_description: Cells were quantified with hek293t cells to facilitate author.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 15
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Andrews, Foster and Johnson #28284-SPACE'
    concentration_or_purity: 96.7%
  - material_name: DMEM
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "14329 x g, 28\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Dennis-James Enough4786
  - equipment_name: Confocal Microscope
    manufacturer_model: Brewer-Brown Rock2693
    settings_parameters: "14887 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate lawyer.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 480
  - step_description: Cells were transfected with anti-ha antibody to facilitate behind.
    conditions_or_variables:
    - adherent culture
    data_collected: false
control_groups:
- control_type: Vehicle Control
  description: Near both future your land yourself out place American institution
    foot shoulder.
- control_type: Positive Control
  description: Mouth need middle rate statement seek travel know.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Joseph Davis
  and results were consistent across multiple biological replicates.
