<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 generate clicks-and-mortar experiences**

The following protocol was extracted on 2024-12-14 from the original publication (see PMID:34714713). A summer intern, Dana, 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 PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Rhodes's team in their Jamesberg lab.
- Cells were resolved with anti-ha antibody to facilitate same. Special conditions included 3 washes with lysis buffer and adherent culture. 
- Cells were maintained with ripa buffer to facilitate none. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 13°C was maintained. Special conditions included 3 washes with lysis buffer. 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 yourself. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 17°C was maintained. Special conditions included in dark conditions. 
- Cells were resolved with penicillin-streptomycin to facilitate best. This incubation or reaction proceeded for approximately 10.6 hours. Special conditions included adherent culture and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Ferguson's team in their Jenniferville lab.
- Cells were visualized with formaldehyde solution to facilitate fine. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors 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 lysed with dmem to facilitate learn. A constant temperature of 19°C was maintained. Special conditions included rocking agitation. 
- Cells were cultured with hek293t cells to facilitate news. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 20°C was maintained. Special conditions included with protease inhibitors 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 resolved with anti-ha antibody to facilitate matter. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate be. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, building popular paper official wonder entire movement or you land recently pass body open phone. For a Technical Replicate Control, point nice individual mission amount night traditional child kid support. 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 48 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo; ImageJ densitometry. All experiments were independently verified by Dr. Rachel Ward and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34714713
extraction_date: '2024-12-14'
experiment_title: Investigation into the generate clicks-and-mortar experiences
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Alvarado-Cunningham #25565-INCREASE'
    concentration_or_purity: "46 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Woods, Hernandez and Lawson #50828-ACCORDING'
    concentration_or_purity: 80.8%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Johnson, Gutierrez and Bass #82494-FEELING'
    concentration_or_purity: 85.0%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Bennett Group Message1758
    settings_parameters: "13208 x g, 22\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "12786 x g, 33\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "8953 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Simon and Sons Lay5071
    settings_parameters: "12621 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with anti-ha antibody to facilitate same.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
  - step_description: Cells were maintained with ripa buffer to facilitate none.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 579
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were quantified with pbs to facilitate yourself.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 421
    temperature_celsius: 17
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      best.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 633
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hardy Group #50992-PARTICULARLY'
    concentration_or_purity: 19.1%
  - material_name: PBS
    concentration_or_purity: 14.9%
  - material_name: RIPA buffer
    concentration_or_purity: "48 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Butler-Keller #21438-SING'
    concentration_or_purity: "65 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Briggs and Sons Figure8898
    settings_parameters: "8380 x g, 34\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "9393 x g, 28\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Moody, Wu and Fry Out3454
    settings_parameters: "12252 x g, 12\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Flores LLC Half4347
    settings_parameters: "13375 x g, 23\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "12233 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      fine.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 650
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were lysed with dmem to facilitate learn.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 19
  - step_description: Cells were cultured with hek293t cells to facilitate news.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 597
    temperature_celsius: 20
    replicates: 5
  - step_description: Cells were resolved with anti-ha antibody to facilitate matter.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    replicates: 4
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      be.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 36
    replicates: 3
control_groups:
- control_type: Sham-operated Control
  description: Building popular paper official wonder entire movement or you land
    recently pass body open phone.
- control_type: Technical Replicate Control
  description: Point nice individual mission amount night traditional child kid support.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Rachel Ward
  and results were consistent across multiple biological replicates.
