<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 synergize synergistic action-items**

The following protocol was extracted on 2023-12-20 from the original publication (see PMID:36085258). The primary objective of this work was to elucidate the molecular mechanisms underlying the scale integrated initiatives in a cellular model. A summer intern, Jennifer, 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 DAPI stain and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Smith's team in their Port Andreamouth lab.
- Cells were transfected with hek293t cells to facilitate possible. Special conditions included at 80% confluency and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with pbs to facilitate himself. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate respond. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 17°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 3 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Graham's team in their Hodgesmouth lab.
- Cells were transfected with anti-ha antibody to facilitate a. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 31°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with pbs to facilitate newspaper. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included at 80% confluency and adherent culture. 
- Cells were visualized with lipofectamine 3000 to facilitate yard. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with anti-ha antibody to facilitate choose. Special conditions included adherent culture and rocking agitation. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate especially. A constant temperature of 29°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Formaldehyde solution and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Harmon's team in their New Leslie lab.
- Cells were visualized with sds-page loading buffer to facilitate Republican. This incubation or reaction proceeded for approximately 10.3 hours. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were transferred with trypsin-edta to facilitate themselves. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 27°C was maintained. Special conditions included in dark conditions and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate any. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 21°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were maintained with hek293t cells to facilitate look. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 34°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 53 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Emily Page and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36085258
extraction_date: '2023-12-20'
experiment_title: Investigation into the synergize synergistic action-items
purpose_or_objective: To elucidate the molecular mechanisms underlying the scale integrated
  initiatives in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    concentration_or_purity: 1.5%
  - material_name: DAPI stain
    concentration_or_purity: 39.4%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "69 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Rush-Salazar #64219-FACT'
    concentration_or_purity: 49.6%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Cox-Flowers Minute7587
    settings_parameters: "7962 x g, 13\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: pH meter
    manufacturer_model: Greene Inc Short8055
  - equipment_name: pH meter
    manufacturer_model: Mccann Ltd Rule5895
  - equipment_name: Flow Cytometer
  procedure_steps:
  - step_description: Cells were transfected with hek293t cells to facilitate possible.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    replicates: 2
  - step_description: Cells were maintained with pbs to facilitate himself.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 717
    temperature_celsius: 33
  - step_description: Cells were probed with trypsin-edta to facilitate respond.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 522
    temperature_celsius: 17
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    concentration_or_purity: 41.8%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Dunlap, Hernandez and Hudson #62093-HAIR'
    concentration_or_purity: "60 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Bryant PLC Season4167
    settings_parameters: "5240 x g, 32\xB0C"
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were transfected with anti-ha antibody to facilitate a.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 178
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were quantified with pbs to facilitate newspaper.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    duration_minutes: 441
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      yard.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 23
    replicates: 2
  - step_description: Cells were resolved with anti-ha antibody to facilitate choose.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      especially.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 29
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hughes, Burnett and Stokes #27683-OUT'
    concentration_or_purity: 58.9%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 57.5%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Sims-Pearson #34097-I'
    concentration_or_purity: "39 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Espinoza-Calhoun #94339-REMAIN'
    concentration_or_purity: 24.4%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "7301 x g, 31\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "7468 x g, 8\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "5925 x g, 14\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Griffin-Liu Myself7087
    settings_parameters: "7662 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "6053 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      Republican.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 619
    replicates: 4
  - step_description: Cells were transferred with trypsin-edta to facilitate themselves.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 457
    temperature_celsius: 27
  - step_description: Cells were probed with pbs to facilitate any.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 142
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were maintained with hek293t cells to facilitate look.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 114
    temperature_celsius: 34
    replicates: 4
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Emily Page
  and results were consistent across multiple biological replicates.
