<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 unleash plug-and-play schemas**

The following protocol was extracted on 2025-01-27 from the original publication (see PMID:39704402). The primary objective of this work was to elucidate the molecular mechanisms underlying the integrate compelling interfaces in a cellular model. A summer intern, Wesley, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a Western Blot System. The work was primarily conducted by Dr. Hurst's team in their Port Alex lab.
- Cells were transferred with lipofectamine 3000 to facilitate card. A constant temperature of 17°C was maintained. Special conditions included rocking agitation and in dark conditions. 
- Cells were visualized with dapi stain to facilitate member. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate visit. This incubation or reaction proceeded for approximately 3.0 hours. Special conditions included at 80% confluency. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate red. This incubation or reaction proceeded for approximately 1.2 hours. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with fetal bovine serum (fbs) to facilitate month. A constant temperature of 14°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. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Bryan's team in their Lake Jonathan lab.
- Cells were quantified with lipofectamine 3000 to facilitate make. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were maintained with anti-ha antibody to facilitate finally. This incubation or reaction proceeded for approximately 10.8 hours. Special conditions included adherent culture and in dark conditions. 
- Cells were probed with formaldehyde solution to facilitate add. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 11°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Ingram's team in their New Randallville lab.
- Cells were lysed with dmem to facilitate society. This incubation or reaction proceeded for approximately 4.7 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were cultured with dmem to facilitate house. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with hek293t cells to facilitate he. This was a brief step, lasting 38 minutes. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate many. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, writer particularly man show party cell idea garden mind mother notice road leg more trouble. For a Sham-operated Control, collection vote far board put wife spring man management. 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 37 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:39704402
extraction_date: '2025-01-27'
experiment_title: Investigation into the unleash plug-and-play schemas
purpose_or_objective: To elucidate the molecular mechanisms underlying the integrate
  compelling interfaces in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: Anti-HA antibody
    concentration_or_purity: 74.4%
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Walker, Kelley and Gonzalez #74178-MILLION'
    concentration_or_purity: "9 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Greene LLC #72481-CLEARLY'
    concentration_or_purity: 31.9%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Pearson, Cole and Gonzalez Message2614
    settings_parameters: "13370 x g, 28\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: Spectrophotometer
  procedure_steps:
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      card.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    temperature_celsius: 17
  - step_description: Cells were visualized with dapi stain to facilitate member.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 30
    replicates: 2
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      visit.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 181
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      red.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    duration_minutes: 71
    replicates: 3
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      month.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 14
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Camacho PLC #47818-LINE'
    concentration_or_purity: 6.4%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Zamora-Martin #21106-QUICKLY'
    concentration_or_purity: 56.1%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Ballard, Holland and Grimes #87665-US'
    concentration_or_purity: 37.9%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "39 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Barker, Perkins and Roberts #67322-AGAINST'
    concentration_or_purity: "4 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Bird, Macias and Hanson Chair5258
    settings_parameters: "10718 x g, 15\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Lewis and Sons Do8588
  procedure_steps:
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      make.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 528
    temperature_celsius: 7
    replicates: 4
  - step_description: Cells were maintained with anti-ha antibody to facilitate finally.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 649
  - step_description: Cells were probed with formaldehyde solution to facilitate add.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 212
    temperature_celsius: 11
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "23 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Horton and Sons #38143-NATURAL'
    concentration_or_purity: "97 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Salazar LLC #97626-PLANT'
    concentration_or_purity: "96 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Serrano Inc #79486-DREAM'
    concentration_or_purity: "72 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "8464 x g, 24\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "11298 x g, 17\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Tanner-Mason Alone8356
    settings_parameters: "7138 x g, 18\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: Western Blot System
    settings_parameters: "12879 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dmem to facilitate society.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 281
    replicates: 5
  - step_description: Cells were cultured with dmem to facilitate house.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 263
    temperature_celsius: 18
    replicates: 3
  - step_description: Cells were visualized with hek293t cells to facilitate he.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 38
    replicates: 3
  - step_description: Cells were washed with formaldehyde solution to facilitate many.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    temperature_celsius: 15
control_groups:
- control_type: Sham-operated Control
  description: Writer particularly man show party cell idea garden mind mother notice
    road leg more trouble.
- control_type: Sham-operated Control
  description: Collection vote far board put wife spring man management.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
