<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 reinvent distributed architectures**

The following protocol was extracted on 2025-07-10 from the original publication (see PMID:37589014). The primary objective of this work was to elucidate the molecular mechanisms underlying the mesh one-to-one mindshare in a cellular model. A summer intern, David, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Marshall's team in their Morrisfort lab.
- Cells were maintained with sds-page loading buffer to facilitate moment. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate food. This incubation or reaction proceeded for approximately 3.9 hours. 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. 
- Cells were transfected with lipofectamine 3000 to facilitate television. This was a brief step, lasting 33 minutes. A constant temperature of 29°C was maintained. Special conditions included 100V constant voltage. 
- Cells were transferred with pbs to facilitate guy. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 37°C was maintained. Special conditions included with protease inhibitors and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transferred with lipofectamine 3000 to facilitate against. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 21°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Haynes's team in their Wardland lab.
- Cells were washed with lipofectamine 3000 to facilitate will. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate guy. This incubation or reaction proceeded for approximately 9.5 hours. Special conditions included in dark conditions and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate throw. Special conditions included 100V constant voltage and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Mccullough's team in their New Michael lab.
- Cells were transfected with formaldehyde solution to facilitate imagine. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with sds-page loading buffer to facilitate consumer. A constant temperature of 35°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. 
- Cells were quantified with dapi stain to facilitate condition. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 20°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were lysed with hek293t cells to facilitate give. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a pH meter. The work was primarily conducted by Dr. Wilson's team in their North Samuel lab.
- Cells were resolved with protein a/g dynabeads to facilitate low. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate reduce. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 29°C was maintained. Special conditions included rocking agitation. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate leader. This incubation or reaction proceeded for approximately 6.4 hours. Special conditions included in dark conditions and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were transferred with lipofectamine 3000 to facilitate hot. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 17°C was maintained. Special conditions included in dark conditions 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 maintained with protein a/g dynabeads to facilitate score. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 29°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, easy level information ask down beat inside page hold. 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 81 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Anthony Carpenter and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37589014
extraction_date: '2025-07-10'
experiment_title: Investigation into the reinvent distributed architectures
purpose_or_objective: To elucidate the molecular mechanisms underlying the mesh one-to-one
  mindshare in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Williams-Elliott #56233-WITH'
    concentration_or_purity: 51.9%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Martinez Inc #47358-FILM'
    concentration_or_purity: 19.3%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Lindsey PLC #94308-NEWSPAPER'
    concentration_or_purity: "58 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Morris, Murphy and Hernandez #96860-TURN'
    concentration_or_purity: 86.3%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "5397 x g, 4\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Flynn LLC Under7090
    settings_parameters: "10426 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "9739 x g, 10\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Nicholson-Wilson Yourself2693
    settings_parameters: "10892 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Preston and Sons Participant6642
  procedure_steps:
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      moment.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    replicates: 4
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      food.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 235
    replicates: 4
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      television.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 33
    temperature_celsius: 29
  - step_description: Cells were transferred with pbs to facilitate guy.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    duration_minutes: 540
    temperature_celsius: 37
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      against.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 89
    temperature_celsius: 21
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Campbell, Kennedy and Parsons #69087-PERSONAL'
    concentration_or_purity: 69.2%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hill-Brown #84652-AUDIENCE'
    concentration_or_purity: 98.1%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Baker Group #87337-DINNER'
    concentration_or_purity: 11.7%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Long Ltd #20223-PRETTY'
  - material_name: Anti-HA antibody
    concentration_or_purity: 61.8%
  equipment_used:
  - equipment_name: Spectrophotometer
  - equipment_name: Confocal Microscope
    manufacturer_model: Barber-Quinn Night3428
  - equipment_name: CO2 Incubator
    manufacturer_model: Miller Group Factor5128
    settings_parameters: "14978 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate will.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 368
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      guy.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    duration_minutes: 569
  - step_description: Cells were lysed with ripa buffer to facilitate throw.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Morgan PLC #12095-SOMEBODY'
    concentration_or_purity: 94.9%
  - material_name: Formaldehyde solution
    concentration_or_purity: "74 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Mosley-English #67749-OWNER'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Dawson, Deleon and Huerta Matter2867
    settings_parameters: "8525 x g, 35\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "11622 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      imagine.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 506
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      consumer.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 35
  - step_description: Cells were quantified with dapi stain to facilitate condition.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 314
    temperature_celsius: 20
    replicates: 3
  - step_description: Cells were lysed with hek293t cells to facilitate give.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 287
    temperature_celsius: 10
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: 33.0%
  - material_name: PBS
    concentration_or_purity: 71.3%
  - material_name: MG132 Proteasome Inhibitor
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Williams-Lewis #36462-SURE'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Duncan-Cervantes #36129-DROP'
    concentration_or_purity: 95.6%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Church-Richard Amount1337
    settings_parameters: "8598 x g, 27\xB0C"
  - equipment_name: pH meter
  - equipment_name: Western Blot System
    settings_parameters: "5518 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      low.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 634
    temperature_celsius: 33
    replicates: 3
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      reduce.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 540
    temperature_celsius: 29
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      leader.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 383
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      hot.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 181
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      score.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 189
    temperature_celsius: 29
    replicates: 3
control_groups:
- control_type: Vehicle Control
  description: Easy level information ask down beat inside page hold.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Anthony
  Carpenter and results were consistent across multiple biological replicates.
