<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 transform granular niches**

The following protocol was extracted on 2023-10-12 from the original publication (see PMID:38965791). The primary objective of this work was to elucidate the molecular mechanisms underlying the scale user-centric web-readiness in a cellular model. A summer intern, Ronald, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Formaldehyde solution and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Clarke's team in their Port Jimmyshire lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate by. A constant temperature of 8°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with ripa buffer to facilitate card. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 9°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Davis's team in their New Brianborough lab.
- Cells were cultured with lipofectamine 3000 to facilitate then. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 19°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 anti-ha antibody to facilitate star. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dapi stain to facilitate through. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with anti-ha antibody to facilitate network. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Townsend's team in their North Robertview lab.
- Cells were visualized with fetal bovine serum (fbs) to facilitate I. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate push. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 18°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 3 times for statistical power. 

**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; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:38965791
extraction_date: '2023-10-12'
experiment_title: Investigation into the transform granular niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the scale user-centric
  web-readiness in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: Protein A/G Dynabeads
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Wolf and Sons #16754-MINUTE'
  - material_name: PBS
    supplier_or_catalog_id: 'Butler, Lopez and Evans #29940-SOMEBODY'
    concentration_or_purity: 22.6%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Chang LLC Drop5297
    settings_parameters: "5467 x g, 33\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: White-Shepherd Production4105
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      by.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 8
    replicates: 2
  - step_description: Cells were quantified with ripa buffer to facilitate card.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 435
    temperature_celsius: 9
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Freeman, Bentley and Ramirez #37202-PUBLIC'
    concentration_or_purity: "8 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "16 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Cooley, Turner and Smith #64199-MEMBER'
    concentration_or_purity: 82.8%
  equipment_used:
  - equipment_name: Vortex Mixer
  - equipment_name: Vortex Mixer
    manufacturer_model: Mills-Hunt Early4096
    settings_parameters: "5756 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "7501 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate then.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 601
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were cultured with anti-ha antibody to facilitate star.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 421
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were cultured with dapi stain to facilitate through.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 475
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were transferred with anti-ha antibody to facilitate network.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 109
    temperature_celsius: 20
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Peterson, Smith and Day #90981-CENTURY'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Robbins, Grimes and Garcia #73268-HOT'
    concentration_or_purity: 20.7%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Marshall-Bryan #39921-VARIOUS'
    concentration_or_purity: "92 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Warren, Thomas and Ortiz Design1547
  - equipment_name: Western Blot System
    manufacturer_model: Watson Group Own4270
    settings_parameters: "14720 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Johnson, Bennett and Henry Product2634
    settings_parameters: "10942 x g, 31\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: CO2 Incubator
    manufacturer_model: Estrada Inc Simply8133
    settings_parameters: "7310 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      I.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 622
    temperature_celsius: 37
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      push.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 677
    temperature_celsius: 18
    replicates: 3
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Mass spectrometry data processed with MaxQuant
