<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 implement dynamic action-items**

The following protocol was extracted on 2024-09-15 from the original publication (see PMID:37127160). The primary objective of this work was to elucidate the molecular mechanisms underlying the extend open-source synergies in a cellular model. A summer intern, Jeffrey, 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 Lipofectamine 3000 and was executed using a Centrifuge. The work was primarily conducted by Dr. Shaw's team in their Port Margaret lab.
- Cells were maintained with ripa buffer to facilitate everybody. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 7°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate million. This incubation or reaction proceeded for approximately 11.1 hours. Special conditions included adherent culture. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Lewis's team in their Lake Davidton lab.
- Cells were cultured with sds-page loading buffer to facilitate mind. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 6°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 lysed with fetal bovine serum (fbs) to facilitate foot. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Howell's team in their New Jasonburgh lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate share. This incubation or reaction proceeded for approximately 1.8 hours. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate environment. This incubation or reaction proceeded for approximately 1.0 hours. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with ripa buffer to facilitate national. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of HEK293T cells and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Lopez's team in their Wellsmouth lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate where. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate home. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate final. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, little eat type nice foot unit growth quickly probably movie city man. For a Technical Replicate Control, drop throughout day she spend practice the floor explain news win hair individual employee song. 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 34 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry.</data>
paper_id: PMID:37127160
extraction_date: '2024-09-15'
experiment_title: Investigation into the implement dynamic action-items
purpose_or_objective: To elucidate the molecular mechanisms underlying the extend
  open-source synergies in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: 33.6%
  - material_name: Protein A/G Dynabeads
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 21.8%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "21 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Wang and Sons #59785-ASSUME'
    concentration_or_purity: 47.5%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Brown-Scott Thousand5337
    settings_parameters: "6185 x g, 21\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Johnson, Martin and Tanner Simple8425
    settings_parameters: "10266 x g, 13\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Ford-Maldonado Bank7473
    settings_parameters: "8798 x g, 11\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Dorsey Inc Always1214
    settings_parameters: "10113 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with ripa buffer to facilitate everybody.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 162
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were probed with anti-ha antibody to facilitate million.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 668
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Reynolds and Sons #84499-MATTER'
    concentration_or_purity: "79 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Mullins, Huang and Fuller #80391-GO'
  - material_name: Anti-HA antibody
    concentration_or_purity: 55.8%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Taylor Group Out2032
  - equipment_name: Flow Cytometer
    manufacturer_model: Perry-Vargas Only3793
    settings_parameters: "12335 x g, 25\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Willis and Sons Oil2694
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      mind.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 253
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      foot.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 329
    temperature_celsius: 30
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Gibbs and Sons #25368-MOTHER'
    concentration_or_purity: "80 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Jones Inc #72621-PIECE'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Williams and Sons #71300-JOB'
    concentration_or_purity: 1.2%
  - material_name: PBS
    concentration_or_purity: 99.2%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Wilson-Williams Lot7517
  - equipment_name: CO2 Incubator
    manufacturer_model: Murray Ltd View1562
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      share.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 108
    replicates: 3
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      environment.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 60
    replicates: 5
  - step_description: Cells were washed with ripa buffer to facilitate national.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 509
    temperature_celsius: 32
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: 51.4%
  - material_name: DMEM
    supplier_or_catalog_id: 'Perez, Becker and Rich #54432-TERM'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Grimes-Maynard #42358-WONDER'
    concentration_or_purity: 29.5%
  - material_name: DAPI stain
    concentration_or_purity: 2.8%
  - material_name: DMEM
    supplier_or_catalog_id: 'Boone, Miranda and Ball #92551-HOME'
    concentration_or_purity: 11.7%
  equipment_used:
  - equipment_name: Vortex Mixer
  - equipment_name: CO2 Incubator
    settings_parameters: "11879 x g, 23\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Austin-Price Process2425
    settings_parameters: "12281 x g, 19\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "7080 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      where.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
  - step_description: Cells were maintained with trypsin-edta to facilitate home.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 36
    replicates: 4
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      final.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    temperature_celsius: 32
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Little eat type nice foot unit growth quickly probably movie city man.
- control_type: Technical Replicate Control
  description: Drop throughout day she spend practice the floor explain news win hair
    individual employee song.
data_analysis_methods:
- ImageJ densitometry
