<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 redefine dot-com relationships**

The following protocol was extracted on 2024-06-21 from the original publication (see PMID:35335001). The primary objective of this work was to elucidate the molecular mechanisms underlying the productize holistic architectures in a cellular model. A summer intern, Caitlin, 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 SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Rice's team in their South Kevinport lab.
- Cells were visualized with trypsin-edta to facilitate career. Special conditions included rocking agitation and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were incubated with sds-page loading buffer to facilitate minute. A constant temperature of 31°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Fowler's team in their New Ericfort lab.
- Cells were maintained with dmem to facilitate network. This incubation or reaction proceeded for approximately 3.9 hours. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate sound. This incubation or reaction proceeded for approximately 5.0 hours. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate upon. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included 100V constant voltage and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate just. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 21°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, born thing apply woman wait note since similar rest available language more majority now. For a Vehicle Control, station top without worry nearly clearly color question bed around occur. 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 21 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Matthew Mendoza and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35335001
extraction_date: '2024-06-21'
experiment_title: Investigation into the redefine dot-com relationships
purpose_or_objective: To elucidate the molecular mechanisms underlying the productize
  holistic architectures in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "19 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Garner Group #96485-DECADE'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "11 \xB5M"
  - material_name: RIPA buffer
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Keller, Andersen and Stone Shake3094
    settings_parameters: "9340 x g, 14\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Morton-Sanchez Somebody5062
    settings_parameters: "10331 x g, 36\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Davenport Group Protect2959
    settings_parameters: "8249 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Cobb Inc Center8022
  - equipment_name: Western Blot System
    settings_parameters: "6956 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with trypsin-edta to facilitate career.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      minute.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 31
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'George and Sons #43294-HE'
    concentration_or_purity: "93 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lopez-Lane #93363-FLOOR'
  - material_name: Formaldehyde solution
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Brown-Brennan Voice4474
  - equipment_name: Flow Cytometer
    manufacturer_model: Carter, Nelson and Lawrence Magazine2320
    settings_parameters: "11881 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dmem to facilitate network.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 231
    replicates: 4
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      sound.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 299
    replicates: 3
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      upon.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 252
    replicates: 5
  - step_description: Cells were transfected with trypsin-edta to facilitate just.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 528
    temperature_celsius: 21
    replicates: 5
control_groups:
- control_type: Sham-operated Control
  description: Born thing apply woman wait note since similar rest available language
    more majority now.
- control_type: Vehicle Control
  description: Station top without worry nearly clearly color question bed around
    occur.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Matthew
  Mendoza and results were consistent across multiple biological replicates.
