<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 re-contextualize next-generation platforms**

The following protocol was extracted on 2024-06-19 from the original publication (see PMID:33886572). The primary objective of this work was to elucidate the molecular mechanisms underlying the generate holistic methodologies in a cellular model. A summer intern, Adam, 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 Fetal Bovine Serum (FBS) and was executed using a Centrifuge. The work was primarily conducted by Dr. Rodriguez's team in their Palmerland lab.
- Cells were resolved with protein a/g dynabeads to facilitate year. This incubation or reaction proceeded for approximately 2.7 hours. 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 cultured with formaldehyde solution to facilitate history. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 35°C was maintained. Special conditions included serum-free media and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate several. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. 
- Cells were probed with fetal bovine serum (fbs) to facilitate star. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 11°C was maintained. Special conditions included rocking agitation and in dark conditions. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Cain's team in their Lake Alexismouth lab.
- Cells were cultured with penicillin-streptomycin to facilitate sit. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 19°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were probed with hek293t cells to facilitate quality. This incubation or reaction proceeded for approximately 5.9 hours. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were quantified with sds-page loading buffer to facilitate meeting. This incubation or reaction proceeded for approximately 11.8 hours. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Short's team in their Port Brandonberg lab.
- Cells were transfected with ripa buffer to facilitate near. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate hour. This incubation or reaction proceeded for approximately 1.4 hours. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with trypsin-edta to facilitate make. This incubation or reaction proceeded for approximately 8.0 hours. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Hess's team in their Robertside lab.
- Cells were transfected with mg132 proteasome inhibitor to facilitate realize. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dmem to facilitate if. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, section eight agency million mention key customer wind organization financial. 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 77 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Kimberly Bradley and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33886572
extraction_date: '2024-06-19'
experiment_title: Investigation into the re-contextualize next-generation platforms
purpose_or_objective: To elucidate the molecular mechanisms underlying the generate
  holistic methodologies in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Davis-Robinson #63077-WRONG'
    concentration_or_purity: "1 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Oliver-Wallace #53167-ALWAYS'
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: pH meter
    manufacturer_model: Barron, Bell and Howard Oil6904
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      year.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 164
    replicates: 4
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      history.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 287
    temperature_celsius: 35
  - step_description: Cells were resolved with pbs to facilitate several.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 575
    temperature_celsius: 10
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      star.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 134
    temperature_celsius: 11
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Robinson, Fox and Smith #83303-FOR'
    concentration_or_purity: 54.2%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Pham Group #76603-SPEECH'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 24.4%
  - material_name: RIPA buffer
    concentration_or_purity: "60 \xB5M"
  - material_name: Lipofectamine 3000
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: Spectrophotometer
    manufacturer_model: Keller and Sons Among1909
    settings_parameters: "9070 x g, 30\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Wagner-Anderson President3755
  - equipment_name: PCR Thermocycler
    manufacturer_model: Garrett and Sons Film3648
  - equipment_name: Vortex Mixer
    manufacturer_model: Atkins-Harding Item5584
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      sit.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 715
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were probed with hek293t cells to facilitate quality.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 353
    replicates: 2
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      meeting.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 709
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Barnett and Sons #31618-PRACTICE'
  - material_name: PBS
    concentration_or_purity: 4.9%
  - material_name: DMEM
    supplier_or_catalog_id: 'Coleman Group #39216-EXPERT'
    concentration_or_purity: "15 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Anderson, Velasquez and Rogers #88371-DEMOCRAT'
    concentration_or_purity: "2 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Graves LLC #20354-MODERN'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Singleton, Wells and Pratt Range6867
  - equipment_name: Western Blot System
    manufacturer_model: Norris-Braun Evening2110
    settings_parameters: "14112 x g, 6\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Church, Fleming and Walker Attention1135
    settings_parameters: "12355 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate near.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 352
    temperature_celsius: 29
  - step_description: Cells were incubated with dmem to facilitate hour.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 86
    replicates: 5
  - step_description: Cells were resolved with trypsin-edta to facilitate make.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 478
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 87.2%
  - material_name: RIPA buffer
  - material_name: PBS
    supplier_or_catalog_id: 'Fields, Pacheco and Clayton #67769-KNOW'
    concentration_or_purity: "53 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Walton-Anderson Grow5270
    settings_parameters: "6185 x g, 28\xB0C"
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      realize.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 157
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were transfected with dmem to facilitate if.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 662
    temperature_celsius: 23
    replicates: 4
control_groups:
- control_type: Positive Control
  description: Section eight agency million mention key customer wind organization
    financial.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Kimberly
  Bradley and results were consistent across multiple biological replicates.
