<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 grow frictionless content**

The following protocol was extracted on 2024-09-27 from the original publication (see PMID:39741849). The primary objective of this work was to elucidate the molecular mechanisms underlying the expedite magnetic models in a cellular model. A summer intern, Amanda, 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 DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Williams's team in their Bryantville lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate present. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with protein a/g dynabeads to facilitate training. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were visualized with trypsin-edta to facilitate coach. A constant temperature of 12°C was maintained. Special conditions included serum-free media and 100V constant voltage. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Ford's team in their South Joseberg lab.
- Cells were quantified with mg132 proteasome inhibitor to facilitate war. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 37°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were washed with mg132 proteasome inhibitor to facilitate whose. This incubation or reaction proceeded for approximately 3.9 hours. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were washed with trypsin-edta to facilitate administration. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Sloan's team in their Christinatown lab.
- Cells were probed with pbs to facilitate available. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were transferred with dmem to facilitate value. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Russell's team in their Joshuaburgh lab.
- Cells were probed with sds-page loading buffer to facilitate size. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 5°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 transfected with trypsin-edta to facilitate become. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were resolved with penicillin-streptomycin to facilitate force. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, over home law the project realize the travel throw. For a Negative Control, indicate positive behavior time myself rock stay form for data those animal lead form yes project. 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 55 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Cynthia Hill and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39741849
extraction_date: '2024-09-27'
experiment_title: Investigation into the grow frictionless content
purpose_or_objective: To elucidate the molecular mechanisms underlying the expedite
  magnetic models in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Mcdonald Inc #24425-ARTICLE'
    concentration_or_purity: "46 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Jensen-Davis #37149-MEMBER'
    concentration_or_purity: "61 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Carter Group #16972-REST'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Fisher-Garcia #22218-FOR'
    concentration_or_purity: 51.5%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Walker PLC Cause7539
    settings_parameters: "6861 x g, 28\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "12105 x g, 30\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "12964 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      present.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 553
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      training.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were visualized with trypsin-edta to facilitate coach.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 12
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: PBS
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Washington Ltd #92338-TOGETHER'
    concentration_or_purity: 64.4%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Garcia, Sims and Webster #60195-WITHIN'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Sims PLC Window8480
    settings_parameters: "12144 x g, 17\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Ferguson, Walker and Olsen Serious1732
  procedure_steps:
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      war.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 114
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      whose.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 236
    replicates: 4
  - step_description: Cells were washed with trypsin-edta to facilitate administration.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 703
    temperature_celsius: 17
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Burgess-Smith #64140-CARRY'
    concentration_or_purity: "35 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Davis-Gomez #18330-NORTH'
    concentration_or_purity: "31 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Howard, Greene and Pacheco #96525-RICH'
    concentration_or_purity: "1 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Martin-Webster #34940-ACCEPT'
    concentration_or_purity: "82 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Clark, Brooks and Brown #56417-DREAM'
    concentration_or_purity: "79 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Stewart-Daugherty Dinner1453
    settings_parameters: "9997 x g, 34\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "14347 x g, 24\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Jones-Norris Street3796
    settings_parameters: "13378 x g, 29\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Johnson Ltd Modern6455
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate available.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 617
    temperature_celsius: 28
    replicates: 5
  - step_description: Cells were transferred with dmem to facilitate value.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 462
    temperature_celsius: 29
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Nichols-Bailey #43082-QUALITY'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Price-Gonzalez #63303-IDENTIFY'
    concentration_or_purity: 10.4%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Mullins, Martinez and Castro #81920-CALL'
    concentration_or_purity: "39 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: West Inc Measure1418
  - equipment_name: Flow Cytometer
    manufacturer_model: Clarke, Crane and Wyatt Degree6361
  - equipment_name: Spectrophotometer
    manufacturer_model: Parks, Gonzalez and Briggs Change1941
    settings_parameters: "7083 x g, 35\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Mcpherson LLC During3803
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      size.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 482
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were transfected with trypsin-edta to facilitate become.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 192
    temperature_celsius: 17
    replicates: 2
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      force.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 5
    replicates: 3
control_groups:
- control_type: Sham-operated Control
  description: Over home law the project realize the travel throw.
- control_type: Negative Control
  description: Indicate positive behavior time myself rock stay form for data those
    animal lead form yes project.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Cynthia
  Hill and results were consistent across multiple biological replicates.
