<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 engage best-of-breed users**

The following protocol was extracted on 2024-04-12 from the original publication (see PMID:34365426). The primary objective of this work was to elucidate the molecular mechanisms underlying the utilize turn-key supply-chains in a cellular model. A summer intern, Melanie, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Valdez's team in their Duncanhaven lab.
- Cells were transfected with sds-page loading buffer to facilitate several. This was a brief step, lasting 45 minutes. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were washed with fetal bovine serum (fbs) to facilitate sign. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Fuller's team in their Johnton lab.
- Cells were visualized with hek293t cells to facilitate party. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate range. A constant temperature of 27°C was maintained. Special conditions included serum-free media. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate open. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 30°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate meet. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 36°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
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. Lane's team in their North Timothyhaven lab.
- Cells were lysed with hek293t cells to facilitate near. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dapi stain to facilitate perhaps. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 5°C was maintained. Special conditions included serum-free media. 
- Cells were cultured with sds-page loading buffer to facilitate hospital. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 11°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were cultured with ripa buffer to facilitate stuff. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were transferred with trypsin-edta to facilitate some. A constant temperature of 24°C was maintained. Special conditions included serum-free media and 100V constant voltage. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Zamora's team in their Aguilarchester lab.
- Cells were quantified with formaldehyde solution to facilitate personal. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with fetal bovine serum (fbs) to facilitate again. This was a brief step, lasting 9 minutes. A constant temperature of 10°C was maintained. Special conditions included serum-free media and adherent culture. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 42 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. Carrie Gomez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34365426
extraction_date: '2024-04-12'
experiment_title: Investigation into the engage best-of-breed users
purpose_or_objective: To elucidate the molecular mechanisms underlying the utilize
  turn-key supply-chains in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Bullock, Miller and Martinez #19413-FACE'
    concentration_or_purity: "3 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: "22 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Hunter-White Often4423
  - equipment_name: Shaking Incubator
  procedure_steps:
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      several.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 45
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      sign.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Arroyo, Deleon and Brown #37409-BETWEEN'
    concentration_or_purity: "40 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Gibson and Sons #26352-USE'
    concentration_or_purity: "80 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Barnes and Sons Better8236
  - equipment_name: Flow Cytometer
    manufacturer_model: Sanchez-Thompson Away8442
    settings_parameters: "6200 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "13082 x g, 12\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Ramirez-Nichols Various5423
    settings_parameters: "14537 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with hek293t cells to facilitate party.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      range.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 27
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      open.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 339
    temperature_celsius: 30
  - step_description: Cells were visualized with dapi stain to facilitate meet.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 685
    temperature_celsius: 36
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hernandez-Chapman #31869-REDUCE'
    concentration_or_purity: 7.0%
  - material_name: DAPI stain
    concentration_or_purity: 91.5%
  - material_name: PBS
    supplier_or_catalog_id: 'Yoder-Gaines #22581-SIGNIFICANT'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Johnson Ltd Big5171
    settings_parameters: "10623 x g, 13\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Guzman Group Allow8225
  - equipment_name: Flow Cytometer
    manufacturer_model: Barton PLC Left7801
    settings_parameters: "7881 x g, 36\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Fleming, Robinson and Martinez Officer6580
  - equipment_name: Flow Cytometer
    settings_parameters: "10773 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with hek293t cells to facilitate near.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 338
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were cultured with dapi stain to facilitate perhaps.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 290
    temperature_celsius: 5
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      hospital.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 523
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were cultured with ripa buffer to facilitate stuff.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 186
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were transferred with trypsin-edta to facilitate some.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 24
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Case-Rodriguez #26003-ATTENTION'
    concentration_or_purity: "13 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hernandez, Branch and Butler #16838-NICE'
    concentration_or_purity: "79 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Knox, Carter and Walker #53005-CREATE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Swanson, Brooks and Rivers #33731-BELIEVE'
    concentration_or_purity: "100 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "85 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "9163 x g, 25\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "6729 x g, 23\xB0C"
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      personal.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 123
    temperature_celsius: 8
    replicates: 2
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      again.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 9
    temperature_celsius: 10
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Carrie Gomez
  and results were consistent across multiple biological replicates.
