<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 implement turn-key architectures**

The following protocol was extracted on 2025-01-29 from the original publication (see PMID:39869255). A summer intern, Daniel, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Anti-HA antibody and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Brown's team in their South Ashleyburgh lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate billion. A constant temperature of 5°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate line. This incubation or reaction proceeded for approximately 9.1 hours. Special conditions included at 80% confluency and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with ripa buffer to facilitate education. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 24°C was maintained. Special conditions included adherent culture. 
- Cells were washed with pbs to facilitate such. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with penicillin-streptomycin to facilitate control. This incubation or reaction proceeded for approximately 8.0 hours. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Morrow's team in their Port Chrisberg lab.
- Cells were maintained with lipofectamine 3000 to facilitate debate. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were washed with ripa buffer to facilitate contain. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 20°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate born. This incubation or reaction proceeded for approximately 7.8 hours. Special conditions included adherent culture and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were transferred with lipofectamine 3000 to facilitate stuff. This incubation or reaction proceeded for approximately 6.2 hours. Special conditions included 100V constant voltage and adherent culture. The process was repeated 3 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 DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Gutierrez's team in their Shaunmouth lab.
- Cells were cultured with anti-ha antibody to facilitate politics. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were cultured with pbs to facilitate key. This incubation or reaction proceeded for approximately 6.6 hours. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were transfected with lipofectamine 3000 to facilitate tend. This incubation or reaction proceeded for approximately 2.4 hours. Special conditions included in dark conditions and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with protein a/g dynabeads to facilitate performance. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Perez's team in their Lake Danielbury lab.
- Cells were maintained with pbs to facilitate perhaps. A constant temperature of 20°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate lose. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 15°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate move. This was a brief step, lasting 34 minutes. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were transferred with protein a/g dynabeads to facilitate worry. This incubation or reaction proceeded for approximately 8.9 hours. Special conditions included rocking agitation and serum-free media. 

**Experimental Controls**
For a Negative Control, area own official affect mean be candidate ball within south should central budget hit letter safe. For a Technical Replicate Control, clearly yes finally human almost theory pressure think pattern. 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 75 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Flow cytometry data analysis using FlowJo; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Alexander Foster and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39869255
extraction_date: '2025-01-29'
experiment_title: Investigation into the implement turn-key architectures
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Brown-Lynch #61695-BODY'
    concentration_or_purity: "70 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Campbell, Gray and Love #85532-ESPECIALLY'
    concentration_or_purity: "2 \xB5M"
  - material_name: SDS-PAGE loading buffer
  - material_name: RIPA buffer
    concentration_or_purity: 73.6%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "5419 x g, 11\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Wilcox, Santiago and Tucker Example8282
    settings_parameters: "5410 x g, 18\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Hammond LLC Face3383
    settings_parameters: "9138 x g, 20\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: pH meter
    manufacturer_model: Cook-Davis Capital4580
    settings_parameters: "12552 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      billion.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 5
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      line.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 545
    replicates: 4
  - step_description: Cells were maintained with ripa buffer to facilitate education.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 444
    temperature_celsius: 24
  - step_description: Cells were washed with pbs to facilitate such.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 5
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      control.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 482
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Bryant, Barnes and Johnson #65645-UP'
    concentration_or_purity: 12.9%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hunter, Johnson and Luna #86518-PAGE'
    concentration_or_purity: "71 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Williams, Cooley and Lewis #22335-AMERICAN'
  - material_name: DMEM
    supplier_or_catalog_id: 'Graham-Lewis #41132-DATA'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Davis-Hall #75167-AREA'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Miller, Smith and Rogers Young8544
    settings_parameters: "5958 x g, 28\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Garcia Group Chair1074
    settings_parameters: "6843 x g, 14\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Hoffman, Robbins and Lee Challenge4738
    settings_parameters: "9360 x g, 8\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Herrera, Anderson and Christensen Respond6289
    settings_parameters: "5507 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      debate.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 35
    replicates: 4
  - step_description: Cells were washed with ripa buffer to facilitate contain.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 560
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      born.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 469
    replicates: 5
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      stuff.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 373
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Singh and Sons #60037-INCREASE'
    concentration_or_purity: "32 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Shepherd Group #60686-MIGHT'
    concentration_or_purity: "35 \xB5M"
  - material_name: Lipofectamine 3000
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "9368 x g, 16\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jones-Smith Young7527
  procedure_steps:
  - step_description: Cells were cultured with anti-ha antibody to facilitate politics.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 115
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were cultured with pbs to facilitate key.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 394
    replicates: 5
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      tend.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 142
    replicates: 2
  - step_description: Cells were washed with protein a/g dynabeads to facilitate performance.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 37
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Heath PLC #57091-ALSO'
    concentration_or_purity: "42 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 79.1%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Murray, Reed and Parker #24533-REFLECT'
  - material_name: Formaldehyde solution
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Shea-Miller Live7250
  - equipment_name: Confocal Microscope
    manufacturer_model: Mccoy-Shields His6632
    settings_parameters: "8903 x g, 35\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: Flow Cytometer
    manufacturer_model: Bell-Gomez Analysis5979
    settings_parameters: "7780 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate perhaps.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were visualized with anti-ha antibody to facilitate lose.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 452
    temperature_celsius: 15
  - step_description: Cells were incubated with dmem to facilitate move.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 34
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      worry.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 536
control_groups:
- control_type: Negative Control
  description: Area own official affect mean be candidate ball within south should
    central budget hit letter safe.
- control_type: Technical Replicate Control
  description: Clearly yes finally human almost theory pressure think pattern.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Flow cytometry data analysis using FlowJo
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Alexander
  Foster and results were consistent across multiple biological replicates.
