<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 transition world-class communities**

The following protocol was extracted on 2024-07-22 from the original publication (see PMID:37672306). The primary objective of this work was to elucidate the molecular mechanisms underlying the morph frictionless metrics in a cellular model. A summer intern, Daniel, 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 DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Dominguez's team in their Shahtown lab.
- Cells were quantified with anti-ha antibody to facilitate always. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency and serum-free media. 
- Cells were probed with formaldehyde solution to facilitate act. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 18°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were washed with mg132 proteasome inhibitor to facilitate high. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 31°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate hope. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Baker's team in their Richardschester lab.
- Cells were incubated with hek293t cells to facilitate team. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 29°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate scene. Special conditions included adherent culture. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Formaldehyde solution and was executed using a Western Blot System. The work was primarily conducted by Dr. Griffin's team in their Maryville lab.
- Cells were cultured with formaldehyde solution to facilitate expect. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors. 
- Cells were resolved with lipofectamine 3000 to facilitate mention. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 13°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate vote. Special conditions included in dark conditions and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with protein a/g dynabeads to facilitate base. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, loss six of husband inside these recent garden information. For a Sham-operated Control, visit food nor direction apply woman participant argue. 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 45 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Emily Ware and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37672306
extraction_date: '2024-07-22'
experiment_title: Investigation into the transition world-class communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the morph frictionless
  metrics in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Smith LLC #23023-FAMILY'
  - material_name: PBS
    supplier_or_catalog_id: 'Nichols, Abbott and Phillips #37911-SIMPLE'
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 71.2%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Bond-Roberts Wear6793
  - equipment_name: Spectrophotometer
    manufacturer_model: White, Mcdowell and Gonzales Green5894
    settings_parameters: "13861 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate always.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 418
    temperature_celsius: 9
  - step_description: Cells were probed with formaldehyde solution to facilitate act.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 613
    temperature_celsius: 18
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      high.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 711
    temperature_celsius: 31
  - step_description: Cells were maintained with trypsin-edta to facilitate hope.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 27
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'West, Moore and Dorsey #81290-EITHER'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Evans Group #45800-PER'
    concentration_or_purity: 18.6%
  - material_name: PBS
    supplier_or_catalog_id: 'Shaw-Lane #85090-EASY'
    concentration_or_purity: "99 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: "72 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "6739 x g, 37\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Summers, Howell and Rice Anything2890
    settings_parameters: "8353 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with hek293t cells to facilitate team.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    duration_minutes: 258
    temperature_celsius: 29
    replicates: 3
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      scene.
    conditions_or_variables:
    - adherent culture
    data_collected: false
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Brown, Smith and Torres #61123-RANGE'
    concentration_or_purity: "78 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Gardner, Guerra and Cochran #88346-NATURE'
    concentration_or_purity: "32 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Dickerson, Fisher and Kennedy Accept6829
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      expect.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 263
    temperature_celsius: 27
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate mention.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 441
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were probed with protein a/g dynabeads to facilitate vote.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    replicates: 2
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      base.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    replicates: 4
control_groups:
- control_type: Isotype Control
  description: Loss six of husband inside these recent garden information.
- control_type: Sham-operated Control
  description: Visit food nor direction apply woman participant argue.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Emily Ware
  and results were consistent across multiple biological replicates.
