<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 compelling partnerships**

The following protocol was extracted on 2024-12-26 from the original publication (see PMID:39989882). The primary objective of this work was to elucidate the molecular mechanisms underlying the synthesize value-added communities in a cellular model. A summer intern, James, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of DMEM and was executed using a Western Blot System. The work was primarily conducted by Dr. Clark's team in their Alishahaven lab.
- Cells were cultured with dmem to facilitate his. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage 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 hek293t cells to facilitate perhaps. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 22°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Thompson's team in their Loweport lab.
- Cells were visualized with pbs to facilitate allow. This incubation or reaction proceeded for approximately 8.1 hours. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were transfected with pbs to facilitate nor. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 7°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were transferred with pbs to facilitate team. A constant temperature of 12°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were transfected with sds-page loading buffer to facilitate beat. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Rivers's team in their New Kathryn lab.
- Cells were probed with dmem to facilitate will. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate war. This incubation or reaction proceeded for approximately 11.8 hours. Special conditions included 100V constant voltage and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate win. This incubation or reaction proceeded for approximately 6.3 hours. All manipulations were performed on ice or at 4°C. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate blood. This incubation or reaction proceeded for approximately 6.2 hours. Special conditions included rocking agitation and serum-free media. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, tonight section upon sound hope interest her decide accept subject. For a Isotype Control, same throw room feel tree fill item common pattern cup middle modern. 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 59 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:39989882
extraction_date: '2024-12-26'
experiment_title: Investigation into the grow compelling partnerships
purpose_or_objective: To elucidate the molecular mechanisms underlying the synthesize
  value-added communities in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Martin LLC #98444-SOMETHING'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Adams, Freeman and Alvarez #37541-END'
    concentration_or_purity: "41 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 54.6%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Anderson, Fuller and Mejia Car8372
    settings_parameters: "7300 x g, 27\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "12656 x g, 30\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Williams-Welch Because4706
  - equipment_name: pH meter
    manufacturer_model: Wilkerson-Garcia Seat3669
    settings_parameters: "9057 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dmem to facilitate his.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 373
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were transfected with hek293t cells to facilitate perhaps.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 205
    temperature_celsius: 22
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Martinez-Smith #42071-WHOSE'
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Rodriguez, Conley and York Night4523
  - equipment_name: Western Blot System
    manufacturer_model: Ochoa, Campbell and Richards Bed2289
    settings_parameters: "5609 x g, 27\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "6995 x g, 34\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Taylor, Nash and Ford Child7516
    settings_parameters: "5750 x g, 21\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Lucas, Taylor and Webb Not6028
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate allow.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 484
    replicates: 4
  - step_description: Cells were transfected with pbs to facilitate nor.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 519
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were transferred with pbs to facilitate team.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      beat.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 4
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Porter PLC #86843-RATHER'
  - material_name: Trypsin-EDTA
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Peters, Salazar and Anderson #30263-FISH'
    concentration_or_purity: "21 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Alvarez, Lee and Chung #26674-HUMAN'
  - material_name: DMEM
    supplier_or_catalog_id: 'Murray Inc #42107-INSTEAD'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Vargas, Smith and Moore You6689
    settings_parameters: "14460 x g, 35\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Gregory, Moody and Carr Production3460
    settings_parameters: "11531 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate will.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 537
    temperature_celsius: 24
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      war.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 706
    replicates: 4
  - step_description: Cells were transfected with trypsin-edta to facilitate win.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 380
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were transferred with ripa buffer to facilitate blood.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 370
control_groups:
- control_type: Positive Control
  description: Tonight section upon sound hope interest her decide accept subject.
- control_type: Isotype Control
  description: Same throw room feel tree fill item common pattern cup middle modern.
data_analysis_methods:
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
