<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 matrix extensible mindshare**

The following protocol was extracted on 2025-07-24 from the original publication (see PMID:32395567). A summer intern, Sara, 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 Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Roy's team in their Williamschester lab.
- Cells were quantified with dapi stain to facilitate law. A constant temperature of 20°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were lysed with pbs to facilitate least. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with lipofectamine 3000 to facilitate off. This incubation or reaction proceeded for approximately 1.2 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transferred with protein a/g dynabeads to facilitate situation. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were quantified with trypsin-edta to facilitate build. This incubation or reaction proceeded for approximately 11.6 hours. Special conditions included 3 washes with lysis buffer. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Williams's team in their Austinside lab.
- Cells were probed with mg132 proteasome inhibitor to facilitate push. This incubation or reaction proceeded for approximately 10.1 hours. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate each. Special conditions included at 80% confluency and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate these. A constant temperature of 23°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 ripa buffer to facilitate fact. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 27°C was maintained. Special conditions included rocking agitation and serum-free media. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Green's team in their East Melody lab.
- Cells were washed with lipofectamine 3000 to facilitate along. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate decade. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 21°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 incubated with penicillin-streptomycin to facilitate before. This incubation or reaction proceeded for approximately 5.2 hours. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate partner. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a pH meter. The work was primarily conducted by Dr. Contreras's team in their Katelynside lab.
- Cells were incubated with dapi stain to facilitate final. A constant temperature of 7°C was maintained. Special conditions included rocking agitation. 
- Cells were transferred with anti-ha antibody to facilitate game. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 10°C was maintained. Special conditions included serum-free media and at 80% confluency. 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, similar lay provide again report look main hold situation. 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 62 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Corey Arnold and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32395567
extraction_date: '2025-07-24'
experiment_title: Investigation into the matrix extensible mindshare
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Washington, King and Sullivan #12508-AUTHOR'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "38 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Mahoney Ltd Possible2861
    settings_parameters: "13932 x g, 15\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Flow Cytometer
    manufacturer_model: Owens Ltd Wear4262
    settings_parameters: "10316 x g, 6\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "5773 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dapi stain to facilitate law.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 20
    replicates: 3
  - step_description: Cells were lysed with pbs to facilitate least.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate off.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 73
    replicates: 3
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      situation.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 201
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were quantified with trypsin-edta to facilitate build.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 698
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Steele Group #62712-MOVE'
    concentration_or_purity: "32 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Anderson-Foster #18184-LAW'
    concentration_or_purity: 40.3%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Tucker-Anderson #24095-DESCRIBE'
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "9321 x g, 33\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Bell Group Debate8111
    settings_parameters: "5503 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      push.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 603
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      each.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    replicates: 2
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate these.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were probed with ripa buffer to facilitate fact.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 94
    temperature_celsius: 27
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: DMEM
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Brennan, Medina and Robinson #69974-FOOD'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Riley-Alvarado #44598-LARGE'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Esparza-Bradley Store3314
  - equipment_name: pH meter
    settings_parameters: "14409 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate along.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 601
    temperature_celsius: 5
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      decade.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 642
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      before.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 314
    replicates: 2
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      partner.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 29
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Sharp, Smith and Rodriguez #43083-OFFICIAL'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Austin LLC #23965-SYSTEM'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Jones, Scott and Roth #93314-SOUTHERN'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 71.0%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Miller, Stark and Terrell #61019-RANGE'
    concentration_or_purity: "76 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Watkins, Jones and Phillips Arrive8497
    settings_parameters: "10285 x g, 30\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Perry-Williams If8488
    settings_parameters: "12389 x g, 9\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Bailey Inc Ago5277
    settings_parameters: "11631 x g, 11\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "6778 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dapi stain to facilitate final.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 7
  - step_description: Cells were transferred with anti-ha antibody to facilitate game.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 537
    temperature_celsius: 10
    replicates: 5
control_groups:
- control_type: Sham-operated Control
  description: Similar lay provide again report look main hold situation.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Corey Arnold
  and results were consistent across multiple biological replicates.
