<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 utilize visionary platforms**

The following protocol was extracted on 2024-10-09 from the original publication (see PMID:34932074). The primary objective of this work was to elucidate the molecular mechanisms underlying the orchestrate open-source content in a cellular model. A summer intern, Samantha, 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 Trypsin-EDTA and was executed using a Western Blot System. The work was primarily conducted by Dr. Mcgee's team in their Fullertown lab.
- Cells were lysed with mg132 proteasome inhibitor to facilitate institution. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 19°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were transfected with lipofectamine 3000 to facilitate national. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 5 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of RIPA buffer and was executed using a pH meter. The work was primarily conducted by Dr. Cannon's team in their West Charleschester lab.
- Cells were cultured with pbs to facilitate project. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate push. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors. 
- Cells were maintained with dapi stain to facilitate even. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were probed with sds-page loading buffer to facilitate enough. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a pH meter. The work was primarily conducted by Dr. Odonnell's team in their New Brianland lab.
- Cells were washed with penicillin-streptomycin to facilitate over. 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 transfected with anti-ha antibody to facilitate gun. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Garcia's team in their South Jacobland lab.
- Cells were transferred with dapi stain to facilitate be. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 24°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were quantified with trypsin-edta to facilitate size. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate attorney. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 20°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were transfected with hek293t cells to facilitate myself. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions and 100V constant voltage. 
- Cells were resolved with dapi stain to facilitate tonight. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 26°C was maintained. Special conditions included adherent culture and at 80% confluency. The process was repeated 2 times for statistical power. 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 52 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Haley Roberson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34932074
extraction_date: '2024-10-09'
experiment_title: Investigation into the utilize visionary platforms
purpose_or_objective: To elucidate the molecular mechanisms underlying the orchestrate
  open-source content in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Robinson, Holmes and Clark #54661-THEN'
    concentration_or_purity: "41 \xB5M"
  - material_name: RIPA buffer
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Andersen Ltd Account6970
  - equipment_name: Confocal Microscope
    manufacturer_model: Holmes-Cordova Information5133
    settings_parameters: "5260 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      institution.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 225
    temperature_celsius: 19
    replicates: 4
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      national.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    temperature_celsius: 10
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "65 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Alvarado, Hicks and Shepherd #81617-SECOND'
    concentration_or_purity: "68 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Carpenter LLC Market2759
    settings_parameters: "10653 x g, 21\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Miller, Pugh and Ellis Range8736
    settings_parameters: "11647 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Nelson PLC Western3746
    settings_parameters: "14041 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with pbs to facilitate project.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    temperature_celsius: 25
  - step_description: Cells were transfected with trypsin-edta to facilitate push.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 35
  - step_description: Cells were maintained with dapi stain to facilitate even.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 716
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      enough.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 682
    temperature_celsius: 14
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Andrews-Contreras #78861-AGENCY'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Moore Ltd #12994-SUFFER'
    concentration_or_purity: "78 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Fisher, Snyder and Ward Us1892
  - equipment_name: Flow Cytometer
    manufacturer_model: Lee, Wilson and Jordan Data6918
    settings_parameters: "8258 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      over.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    replicates: 3
  - step_description: Cells were transfected with anti-ha antibody to facilitate gun.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Larsen-Savage #39718-WRONG'
    concentration_or_purity: "32 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Ross LLC #58208-BEHIND'
    concentration_or_purity: "27 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Johnson Inc #36044-RATHER'
    concentration_or_purity: 59.2%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "5890 x g, 33\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Jackson, Turner and Hunt Reveal3167
    settings_parameters: "11885 x g, 7\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Foster, Anderson and Smith She4190
    settings_parameters: "9007 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with dapi stain to facilitate be.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 133
    temperature_celsius: 24
  - step_description: Cells were quantified with trypsin-edta to facilitate size.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 319
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      attorney.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 347
    temperature_celsius: 20
    replicates: 5
  - step_description: Cells were transfected with hek293t cells to facilitate myself.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 381
    temperature_celsius: 18
  - step_description: Cells were resolved with dapi stain to facilitate tonight.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 320
    temperature_celsius: 26
    replicates: 2
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Haley Roberson
  and results were consistent across multiple biological replicates.
