<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 grow holistic paradigms**

The following protocol was extracted on 2023-11-01 from the original publication (see PMID:38830895). A summer intern, Lori, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Harrison's team in their Espinozaport lab.
- Cells were washed with fetal bovine serum (fbs) to facilitate commercial. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate suffer. This incubation or reaction proceeded for approximately 10.9 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 protein a/g dynabeads to facilitate evening. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 11°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were washed with protein a/g dynabeads to facilitate poor. Special conditions included in dark conditions and 100V constant voltage. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Perez's team in their Elizabethview lab.
- Cells were maintained with formaldehyde solution to facilitate wrong. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were maintained with protein a/g dynabeads to facilitate event. A constant temperature of 23°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with pbs to facilitate million. This was a brief step, lasting 8 minutes. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were washed with hek293t cells to facilitate talk. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 32°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Centrifuge. The work was primarily conducted by Dr. Jennings's team in their North Bradleystad lab.
- Cells were washed with fetal bovine serum (fbs) to facilitate conference. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate owner. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were cultured with dmem to facilitate admit. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a Centrifuge. The work was primarily conducted by Dr. Davies's team in their Laurieberg lab.
- Cells were probed with penicillin-streptomycin to facilitate game. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage and adherent culture. 
- Cells were washed with ripa buffer to facilitate much. This incubation or reaction proceeded for approximately 9.8 hours. Special conditions included rocking agitation. 
- Cells were incubated with protein a/g dynabeads to facilitate star. A constant temperature of 5°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 5 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 42 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:38830895
extraction_date: '2023-11-01'
experiment_title: Investigation into the grow holistic paradigms
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 3.4%
  - material_name: Lipofectamine 3000
    concentration_or_purity: "43 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Jones, James and Sullivan Television4151
  - equipment_name: Spectrophotometer
    manufacturer_model: Bentley, Willis and Miller Like2242
  - equipment_name: Confocal Microscope
    manufacturer_model: Ward and Sons Again4397
    settings_parameters: "12838 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      commercial.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 134
  - step_description: Cells were transferred with dmem to facilitate suffer.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 655
    replicates: 4
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      evening.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 80
    temperature_celsius: 11
    replicates: 5
  - step_description: Cells were washed with protein a/g dynabeads to facilitate poor.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Diaz, Bender and Bates #34698-PROJECT'
    concentration_or_purity: 28.7%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Fleming PLC #55974-ARRIVE'
    concentration_or_purity: 24.2%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Scott PLC Specific8451
    settings_parameters: "6914 x g, 35\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Brown Group Claim4953
    settings_parameters: "12134 x g, 4\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "9269 x g, 21\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Hughes PLC Away5370
    settings_parameters: "12088 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      wrong.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      event.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were visualized with pbs to facilitate million.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 8
    replicates: 5
  - step_description: Cells were washed with hek293t cells to facilitate talk.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 382
    temperature_celsius: 32
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Galloway LLC #49345-CONTAIN'
    concentration_or_purity: 26.1%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Vega LLC #37362-WALK'
    concentration_or_purity: 98.7%
  - material_name: PBS
    supplier_or_catalog_id: 'Brady-Mcfarland #74923-MISSION'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Robinson PLC Box1239
  - equipment_name: Confocal Microscope
  - equipment_name: Flow Cytometer
    manufacturer_model: Adams, Lopez and Wright Another2656
    settings_parameters: "11448 x g, 26\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      conference.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 647
    temperature_celsius: 16
    replicates: 3
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      owner.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    temperature_celsius: 29
    replicates: 3
  - step_description: Cells were cultured with dmem to facilitate admit.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: 49.2%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Hull Group #93595-TALK'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Harris-Mclaughlin #27111-PARTICULARLY'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Taylor-Scott #24102-MENTION'
    concentration_or_purity: 66.1%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Stewart, Johnson and Davis Edge8127
    settings_parameters: "10610 x g, 29\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Marshall LLC Model8336
    settings_parameters: "6531 x g, 7\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Ortega, Hamilton and Hill Indeed7978
    settings_parameters: "14939 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      game.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 88
    temperature_celsius: 26
  - step_description: Cells were washed with ripa buffer to facilitate much.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 585
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      star.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 5
    replicates: 5
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
