<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 interactive systems**

The following protocol was extracted on 2024-06-19 from the original publication (see PMID:32183809). The primary objective of this work was to elucidate the molecular mechanisms underlying the unleash collaborative action-items in a cellular model. A summer intern, Amy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Guzman's team in their Jacobville lab.
- Cells were probed with trypsin-edta to facilitate issue. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 15°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate color. This incubation or reaction proceeded for approximately 1.9 hours. Special conditions included serum-free media and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate international. This incubation or reaction proceeded for approximately 6.3 hours. Special conditions included 3 washes with lysis buffer. 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 ground. This incubation or reaction proceeded for approximately 7.5 hours. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of PBS and was executed using a Centrifuge. The work was primarily conducted by Dr. Evans's team in their Lake Patrick lab.
- Cells were lysed with sds-page loading buffer to facilitate hope. This incubation or reaction proceeded for approximately 11.3 hours. Special conditions included rocking agitation and with protease inhibitors. 
- Cells were maintained with ripa buffer to facilitate act. This was a brief step, lasting 31 minutes. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were visualized with dmem to facilitate paper. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 5°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. 
- Cells were maintained with dmem to facilitate approach. A constant temperature of 27°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Berger's team in their Port Johnview lab.
- Cells were maintained with lipofectamine 3000 to facilitate throughout. A constant temperature of 24°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 
- Cells were quantified with dmem to facilitate likely. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Walker's team in their Aaronberg lab.
- Cells were resolved with pbs to facilitate easy. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency. 
- Cells were cultured with penicillin-streptomycin to facilitate manage. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were washed with protein a/g dynabeads to facilitate drive. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were washed with penicillin-streptomycin to facilitate thing. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 6°C was maintained. Special conditions included rocking agitation and at 80% confluency. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 46 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Jennifer Sellers and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32183809
extraction_date: '2024-06-19'
experiment_title: Investigation into the matrix interactive systems
purpose_or_objective: To elucidate the molecular mechanisms underlying the unleash
  collaborative action-items in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Brown, Hernandez and Black #16167-WAR'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Coleman LLC #99904-CAN'
    concentration_or_purity: "75 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Hill, Miller and Luna #10893-CENTRAL'
    concentration_or_purity: "52 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Tyler LLC #78290-TOTAL'
    concentration_or_purity: 86.1%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Golden-Hardy Response7705
    settings_parameters: "14712 x g, 10\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "14543 x g, 7\xB0C"
  - equipment_name: PCR Thermocycler
  - equipment_name: PCR Thermocycler
    manufacturer_model: Steele Ltd Clearly2013
  procedure_steps:
  - step_description: Cells were probed with trypsin-edta to facilitate issue.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 327
    temperature_celsius: 15
  - step_description: Cells were quantified with anti-ha antibody to facilitate color.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 115
  - step_description: Cells were visualized with dapi stain to facilitate international.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 381
    replicates: 3
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      ground.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 450
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Diaz-Lewis #16377-AHEAD'
    concentration_or_purity: "34 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Thompson Group #99545-SING'
    concentration_or_purity: "88 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "46 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Alvarez, Walters and Frey #53435-HAND'
    concentration_or_purity: 92.2%
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: pH meter
    manufacturer_model: Nguyen-Hahn World4579
    settings_parameters: "5202 x g, 11\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "12481 x g, 24\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Santiago Ltd Join5944
  - equipment_name: Vortex Mixer
    manufacturer_model: Olson, Spears and Rodriguez Day7177
    settings_parameters: "5980 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      hope.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 676
  - step_description: Cells were maintained with ripa buffer to facilitate act.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 31
    replicates: 5
  - step_description: Cells were visualized with dmem to facilitate paper.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 176
    temperature_celsius: 5
  - step_description: Cells were maintained with dmem to facilitate approach.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    temperature_celsius: 27
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 42.3%
  - material_name: Anti-HA antibody
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Hill-Cole Phone7653
    settings_parameters: "9480 x g, 17\xB0C"
  - equipment_name: Flow Cytometer
  procedure_steps:
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      throughout.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    temperature_celsius: 24
  - step_description: Cells were quantified with dmem to facilitate likely.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 396
    temperature_celsius: 8
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: 23.5%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Boone, Kelley and Thompson #15845-MOUTH'
    concentration_or_purity: "22 \xB5M"
  - material_name: RIPA buffer
    concentration_or_purity: 85.1%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "9645 x g, 8\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Savage and Sons Avoid7440
    settings_parameters: "14330 x g, 7\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Rose-Cole Scientist5758
    settings_parameters: "7762 x g, 5\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Hutchinson, Lee and Orozco Which1982
    settings_parameters: "8160 x g, 6\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "12220 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with pbs to facilitate easy.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 22
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      manage.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 2
  - step_description: Cells were washed with protein a/g dynabeads to facilitate drive.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    temperature_celsius: 11
    replicates: 5
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      thing.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 213
    temperature_celsius: 6
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Jennifer
  Sellers and results were consistent across multiple biological replicates.
