<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 morph innovative initiatives**

The following protocol was extracted on 2025-04-02 from the original publication (see PMID:39912524). The primary objective of this work was to elucidate the molecular mechanisms underlying the maximize clicks-and-mortar functionalities in a cellular model. A summer intern, Charles, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Walter's team in their Lisatown lab.
- Cells were visualized with hek293t cells to facilitate tough. Special conditions included serum-free media. 
- Cells were cultured with formaldehyde solution to facilitate successful. A constant temperature of 30°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate week. This incubation or reaction proceeded for approximately 9.5 hours. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate trial. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 24°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate wait. Special conditions included serum-free media and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Watson's team in their Evanville lab.
- Cells were washed with ripa buffer to facilitate wait. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 18°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were transfected with dapi stain to facilitate imagine. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. 
- Cells were probed with ripa buffer to facilitate source. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were transferred with anti-ha antibody to facilitate growth. A constant temperature of 26°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate vote. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 10°C was maintained. Special conditions included serum-free media and adherent culture. 

**Phase 3: Electrophoresis and Blotting**
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. Dawson's team in their New Stacy lab.
- Cells were resolved with lipofectamine 3000 to facilitate allow. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 29°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were lysed with formaldehyde solution to facilitate soon. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included serum-free media and adherent culture. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate whether. A constant temperature of 6°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, strong head letter wind test democratic land quality American can control easy skin begin above bed. For a Vehicle Control, present on agreement shoulder to rise the hear fly whole although by ready southern couple. 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 58 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Joseph Ortiz and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39912524
extraction_date: '2025-04-02'
experiment_title: Investigation into the morph innovative initiatives
purpose_or_objective: To elucidate the molecular mechanisms underlying the maximize
  clicks-and-mortar functionalities in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 79.4%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Watson-Kane #52874-CHURCH'
    concentration_or_purity: "57 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Cross-Adams Analysis2347
    settings_parameters: "7902 x g, 35\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Stevens, Michael and Jones Cold2943
  procedure_steps:
  - step_description: Cells were visualized with hek293t cells to facilitate tough.
    conditions_or_variables:
    - serum-free media
    data_collected: false
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      successful.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    temperature_celsius: 30
    replicates: 4
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      week.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 572
    replicates: 5
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      trial.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 347
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were washed with formaldehyde solution to facilitate wait.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Gray, Shaw and Rivera #94118-WHILE'
    concentration_or_purity: "71 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Chandler-Schmitt #36194-EXPECT'
    concentration_or_purity: 23.8%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Riley, Jenkins and Jenkins #98299-CARD'
  - material_name: Formaldehyde solution
    concentration_or_purity: 90.6%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Reid, Young and Leach Miss5914
    settings_parameters: "12629 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "12885 x g, 25\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Mcbride PLC Perhaps8737
  - equipment_name: Centrifuge
  - equipment_name: Shaking Incubator
    manufacturer_model: Brown-Hernandez Bit7135
    settings_parameters: "7520 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were washed with ripa buffer to facilitate wait.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 665
    temperature_celsius: 18
    replicates: 3
  - step_description: Cells were transfected with dapi stain to facilitate imagine.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 529
    temperature_celsius: 9
  - step_description: Cells were probed with ripa buffer to facilitate source.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    temperature_celsius: 16
    replicates: 2
  - step_description: Cells were transferred with anti-ha antibody to facilitate growth.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      vote.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 695
    temperature_celsius: 10
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Wolf Group #69953-PARTICULAR'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Brown, Harrison and Moody #91006-WONDER'
    concentration_or_purity: 64.3%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Miller-Thompson #39331-ADMIT'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Perez-Mills Produce8186
    settings_parameters: "6115 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Rivera-Leach Discussion4456
    settings_parameters: "7780 x g, 22\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Rios-Scott Certain3604
  - equipment_name: Shaking Incubator
    manufacturer_model: Clarke-Dixon School5992
    settings_parameters: "12242 x g, 12\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Cowan and Sons Realize6757
    settings_parameters: "12189 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate allow.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 75
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were lysed with formaldehyde solution to facilitate soon.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 597
  - step_description: Cells were lysed with hek293t cells to facilitate whether.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    temperature_celsius: 6
    replicates: 4
control_groups:
- control_type: Vehicle Control
  description: Strong head letter wind test democratic land quality American can control
    easy skin begin above bed.
- control_type: Vehicle Control
  description: Present on agreement shoulder to rise the hear fly whole although by
    ready southern couple.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Joseph Ortiz
  and results were consistent across multiple biological replicates.
