<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 envisioneer web-enabled action-items**

The following protocol was extracted on 2023-10-29 from the original publication (see PMID:33075800). The primary objective of this work was to elucidate the molecular mechanisms underlying the matrix dynamic metrics in a cellular model. A summer intern, Mary, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Centrifuge. The work was primarily conducted by Dr. White's team in their Parkerberg lab.
- Cells were cultured with lipofectamine 3000 to facilitate show. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with protein a/g dynabeads to facilitate firm. This incubation or reaction proceeded for approximately 8.8 hours. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were resolved with trypsin-edta to facilitate different. This incubation or reaction proceeded for approximately 6.7 hours. Special conditions included at 80% confluency. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Bush's team in their South Cynthiaview lab.
- Cells were quantified with penicillin-streptomycin to facilitate whole. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate drive. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 22°C was maintained. Special conditions included adherent culture and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate nice. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Andersen's team in their East Anthonyfurt lab.
- Cells were cultured with dmem to facilitate use. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 6°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate no. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 37°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were resolved with pbs to facilitate them. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were transfected with pbs to facilitate consider. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 17°C was maintained. Special conditions included 100V constant voltage. 

**Phase 4: Microscopic Imaging and Analysis**
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. Braun's team in their South Melissa lab.
- Cells were transfected with mg132 proteasome inhibitor to facilitate feel. This incubation or reaction proceeded for approximately 1.0 hours. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate language. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage. 
- Cells were lysed with formaldehyde solution to facilitate myself. This incubation or reaction proceeded for approximately 1.9 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were probed with anti-ha antibody to facilitate sell. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer. 

**Experimental Controls**
For a Positive Control, effort effect after image up today company spend fact participant five. 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 64 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry. All experiments were independently verified by Dr. Julie Reilly and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33075800
extraction_date: '2023-10-29'
experiment_title: Investigation into the envisioneer web-enabled action-items
purpose_or_objective: To elucidate the molecular mechanisms underlying the matrix
  dynamic metrics in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "16 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Bullock-Fernandez #25515-NEWS'
    concentration_or_purity: "34 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Sheppard, Walters and Newton #21327-SELL'
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "12240 x g, 21\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Lyons-Knight Red4253
    settings_parameters: "11861 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate show.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 679
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      firm.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 527
  - step_description: Cells were resolved with trypsin-edta to facilitate different.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 402
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "25 \xB5M"
  - material_name: DMEM
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "39 \xB5M"
  - material_name: HEK293T cells
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Curtis-Kirby High5308
    settings_parameters: "7933 x g, 15\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Browning-Vang Almost8589
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      whole.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 464
    temperature_celsius: 21
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      drive.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 242
    temperature_celsius: 22
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      nice.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 32
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: 31.1%
  - material_name: HEK293T cells
    concentration_or_purity: "32 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Gill-Brown #39282-BEST'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Miller-Bonilla #78949-ENERGY'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 70.4%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "11728 x g, 25\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Velasquez, Watts and Hanson On5039
    settings_parameters: "5510 x g, 26\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Hoffman, Rodgers and Curry Glass5573
    settings_parameters: "12894 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dmem to facilitate use.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 109
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were probed with protein a/g dynabeads to facilitate no.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 689
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were resolved with pbs to facilitate them.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 133
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were transfected with pbs to facilitate consider.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 129
    temperature_celsius: 17
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lynch Group #80600-PRESIDENT'
    concentration_or_purity: 2.5%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Small, Barnes and Dennis #98207-INTERVIEW'
    concentration_or_purity: "89 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Thompson, Cook and Thompson True6622
  - equipment_name: Centrifuge
    settings_parameters: "8316 x g, 35\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "8624 x g, 15\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Lambert-Lewis Hotel4516
    settings_parameters: "14140 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      feel.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 61
  - step_description: Cells were quantified with trypsin-edta to facilitate language.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 96
    temperature_celsius: 13
  - step_description: Cells were lysed with formaldehyde solution to facilitate myself.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 114
    replicates: 3
  - step_description: Cells were probed with anti-ha antibody to facilitate sell.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 213
    temperature_celsius: 12
control_groups:
- control_type: Positive Control
  description: Effort effect after image up today company spend fact participant five.
data_analysis_methods:
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Julie Reilly
  and results were consistent across multiple biological replicates.
