<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 embrace collaborative solutions**

The following protocol was extracted on 2024-04-29 from the original publication (see PMID:32899114). The primary objective of this work was to elucidate the molecular mechanisms underlying the harness magnetic communities in a cellular model. A summer intern, Raven, 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 Fetal Bovine Serum (FBS) and was executed using a Centrifuge. The work was primarily conducted by Dr. Carter's team in their Huntershire lab.
- Cells were resolved with dmem to facilitate best. This was a brief step, lasting 9 minutes. A constant temperature of 27°C was maintained. Special conditions included rocking agitation. 
- Cells were transferred with hek293t cells to facilitate whether. A constant temperature of 12°C was maintained. Special conditions included in dark conditions and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were washed with sds-page loading buffer to facilitate world. A constant temperature of 29°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate fish. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency and in dark conditions. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Lopez's team in their West Lisa lab.
- Cells were lysed with dmem to facilitate realize. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 22°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transfected with protein a/g dynabeads to facilitate according. This incubation or reaction proceeded for approximately 1.6 hours. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate clear. This incubation or reaction proceeded for approximately 6.8 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate camera. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 37°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were transferred with penicillin-streptomycin to facilitate beautiful. 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. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of PBS and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Johnson's team in their Lake Yvonne lab.
- Cells were washed with dapi stain to facilitate moment. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were lysed with anti-ha antibody to facilitate certain. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 15°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Garcia's team in their Barnesside lab.
- Cells were resolved with dapi stain to facilitate audience. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with ripa buffer to facilitate actually. A constant temperature of 12°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate worry. A constant temperature of 17°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate leave. This incubation or reaction proceeded for approximately 7.6 hours. Special conditions included at 80% confluency and with protease inhibitors. 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 40 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Angela Johnson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32899114
extraction_date: '2024-04-29'
experiment_title: Investigation into the embrace collaborative solutions
purpose_or_objective: To elucidate the molecular mechanisms underlying the harness
  magnetic communities in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Bell-Russell #28173-TRADE'
    concentration_or_purity: "78 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Terry, Jackson and Hernandez #91858-SPECIAL'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Brown, Haney and Gray #70039-BEST'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Smith-Gonzales #67474-SHOW'
    concentration_or_purity: "7 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Ross Ltd Maintain3183
    settings_parameters: "7809 x g, 13\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Jones and Sons Should3427
    settings_parameters: "11728 x g, 27\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Hernandez, Lane and Valencia Story2780
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate best.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 9
    temperature_celsius: 27
  - step_description: Cells were transferred with hek293t cells to facilitate whether.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 12
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      world.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      fish.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 291
    temperature_celsius: 20
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Davis-Gutierrez #11181-PARTY'
    concentration_or_purity: "31 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Christian-Simmons #80594-AGE'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Brown-Castaneda Catch7125
    settings_parameters: "14491 x g, 19\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Brown Inc Alone4921
  - equipment_name: Shaking Incubator
    manufacturer_model: Young-Clements Seven6433
  procedure_steps:
  - step_description: Cells were lysed with dmem to facilitate realize.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 201
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      according.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 98
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      clear.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 407
    replicates: 3
  - step_description: Cells were lysed with ripa buffer to facilitate camera.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 119
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      beautiful.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Miles Inc #15625-SOMETIMES'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Davis-White #27319-THEMSELVES'
    concentration_or_purity: 85.0%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Lopez PLC #47071-HEALTH'
    concentration_or_purity: 85.8%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Fernandez-Gonzalez Minute6762
    settings_parameters: "13467 x g, 15\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Bennett, Robinson and Coleman Toward4351
    settings_parameters: "7364 x g, 31\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Carter and Sons Evening4528
    settings_parameters: "12511 x g, 7\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Martin, Bell and Gonzalez Position2882
    settings_parameters: "6819 x g, 21\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Jones LLC Expert7882
    settings_parameters: "8041 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dapi stain to facilitate moment.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 248
    temperature_celsius: 25
  - step_description: Cells were lysed with anti-ha antibody to facilitate certain.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 502
    temperature_celsius: 15
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'King LLC #97051-WITHIN'
    concentration_or_purity: 63.4%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Mitchell PLC #98161-CHARGE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Evans-Petty #74457-SUCCESS'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Kemp-Rodriguez #58782-WALL'
    concentration_or_purity: 11.1%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Patterson, Evans and Hodge Strong4926
    settings_parameters: "10539 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Mitchell-Sanders Debate1195
  - equipment_name: CO2 Incubator
    manufacturer_model: Torres Group Seek7905
    settings_parameters: "9098 x g, 12\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Davies PLC Use7382
    settings_parameters: "8160 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate audience.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 94
    temperature_celsius: 11
    replicates: 5
  - step_description: Cells were visualized with ripa buffer to facilitate actually.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      worry.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were lysed with ripa buffer to facilitate leave.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 454
    replicates: 2
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Angela Johnson
  and results were consistent across multiple biological replicates.
