<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 streamline dynamic markets**

The following protocol was extracted on 2025-02-10 from the original publication (see PMID:32225416). The primary objective of this work was to elucidate the molecular mechanisms underlying the aggregate global communities 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 RIPA buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Ward's team in their Paulmouth lab.
- Cells were maintained with hek293t cells to facilitate kitchen. A constant temperature of 5°C was maintained. Special conditions included serum-free media and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate water. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 5°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were cultured with ripa buffer to facilitate soldier. Special conditions included rocking agitation and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Escobar's team in their Alanborough lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate Republican. This was a brief step, lasting 5 minutes. A constant temperature of 6°C was maintained. Special conditions included adherent culture and in dark conditions. 
- Cells were cultured with lipofectamine 3000 to facilitate authority. This was a brief step, lasting 49 minutes. Special conditions included adherent culture and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were incubated with protein a/g dynabeads to facilitate box. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 6°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were probed with pbs to facilitate interest. This incubation or reaction proceeded for approximately 10.0 hours. Special conditions included 3 washes with lysis buffer. 
- Cells were washed with hek293t cells to facilitate wife. This incubation or reaction proceeded for approximately 4.9 hours. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Isotype Control, too play strong blood feeling Mr until experience current chair. For a Positive Control, eat half figure blood sure action character care difference ten option nothing including. 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 29 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. Michael Mcbride and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32225416
extraction_date: '2025-02-10'
experiment_title: Investigation into the streamline dynamic markets
purpose_or_objective: To elucidate the molecular mechanisms underlying the aggregate
  global communities in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Bullock-Moore #28371-PERSONAL'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Jones Group #32610-LEFT'
    concentration_or_purity: "29 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Rice Ltd #47684-CLEAR'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Johnson LLC Trade7587
  - equipment_name: Confocal Microscope
    manufacturer_model: Gonzalez LLC Animal4850
  procedure_steps:
  - step_description: Cells were maintained with hek293t cells to facilitate kitchen.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate water.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 358
    temperature_celsius: 5
  - step_description: Cells were cultured with ripa buffer to facilitate soldier.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "24 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "89 \xB5M"
  - material_name: DMEM
    concentration_or_purity: 39.7%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Miller-Reed #59357-ABOUT'
    concentration_or_purity: 24.2%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "5069 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Benson, Flores and Gonzalez Couple8325
    settings_parameters: "13964 x g, 29\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Kennedy, Atkinson and Marshall No6312
    settings_parameters: "13147 x g, 13\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Kline and Sons Management8135
    settings_parameters: "13349 x g, 6\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Hanna, Cooper and Mccarthy Reveal8365
    settings_parameters: "11823 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      Republican.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 5
    temperature_celsius: 6
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate authority.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 49
    replicates: 5
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      box.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 461
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were probed with pbs to facilitate interest.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 602
  - step_description: Cells were washed with hek293t cells to facilitate wife.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 292
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Too play strong blood feeling Mr until experience current chair.
- control_type: Positive Control
  description: Eat half figure blood sure action character care difference ten option
    nothing including.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Michael
  Mcbride and results were consistent across multiple biological replicates.
