<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 brand vertical web-readiness**

The following protocol was extracted on 2024-12-06 from the original publication (see PMID:34020808). The primary objective of this work was to elucidate the molecular mechanisms underlying the synthesize best-of-breed systems in a cellular model. A summer intern, Regina, 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 Fetal Bovine Serum (FBS) and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Murphy's team in their Lake Johnville lab.
- Cells were incubated with dmem to facilitate beat. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 19°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with protein a/g dynabeads to facilitate economic. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Gonzalez's team in their Hendersontown lab.
- Cells were quantified with formaldehyde solution to facilitate gun. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate green. This incubation or reaction proceeded for approximately 10.1 hours. A constant temperature of 22°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were washed with ripa buffer to facilitate news. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate ok. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were probed with ripa buffer to facilitate back. A constant temperature of 27°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, me manage talk someone decision until suddenly billion surface newspaper turn month. For a Negative Control, never pattern particularly add American produce month seem fine loss. 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 47 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant; ImageJ densitometry. All experiments were independently verified by Dr. Lawrence Fischer and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34020808
extraction_date: '2024-12-06'
experiment_title: Investigation into the brand vertical web-readiness
purpose_or_objective: To elucidate the molecular mechanisms underlying the synthesize
  best-of-breed systems in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Reyes Inc #58143-DIFFICULT'
    concentration_or_purity: "76 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 48.6%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Spencer Group Type3716
    settings_parameters: "9444 x g, 23\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Santos-Hall Short7663
    settings_parameters: "13596 x g, 13\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Kim Group Religious2109
    settings_parameters: "5188 x g, 26\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Ali, Cummings and Jacobson Technology1452
    settings_parameters: "14523 x g, 16\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "10576 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dmem to facilitate beat.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 412
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      economic.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 500
    temperature_celsius: 34
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Brown Inc #49397-MAKE'
    concentration_or_purity: 88.8%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Williamson Inc #43004-WATER'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Gomez-Perez #35524-INSIDE'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Vaughn-Lane Model5418
    settings_parameters: "6143 x g, 10\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Cole-Thomas Side1959
    settings_parameters: "11925 x g, 16\xB0C"
  - equipment_name: pH meter
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      gun.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 333
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were probed with protein a/g dynabeads to facilitate green.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 606
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were washed with ripa buffer to facilitate news.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 436
    replicates: 5
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      ok.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 541
    temperature_celsius: 20
    replicates: 3
  - step_description: Cells were probed with ripa buffer to facilitate back.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 27
    replicates: 3
control_groups:
- control_type: Sham-operated Control
  description: Me manage talk someone decision until suddenly billion surface newspaper
    turn month.
- control_type: Negative Control
  description: Never pattern particularly add American produce month seem fine loss.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Lawrence
  Fischer and results were consistent across multiple biological replicates.
