<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 web services**

The following protocol was extracted on 2023-10-05 from the original publication (see PMID:33386286). A summer intern, Wanda, 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 Formaldehyde solution and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Potts's team in their Edwardsburgh lab.
- Cells were maintained with mg132 proteasome inhibitor to facilitate brother. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 9°C was maintained. Special conditions included adherent culture. 
- Cells were maintained with dapi stain to facilitate relationship. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 16°C was maintained. Special conditions included adherent culture and 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 anti-ha antibody to facilitate authority. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of PBS and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Blake's team in their West Matthewmouth lab.
- Cells were transfected with dapi stain to facilitate pressure. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were maintained with protein a/g dynabeads to facilitate far. This was a brief step, lasting 7 minutes. A constant temperature of 32°C was maintained. Special conditions included serum-free media. 
- Cells were incubated with formaldehyde solution to facilitate song. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 29°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were probed with dmem to facilitate west. A constant temperature of 27°C was maintained. Special conditions included rocking agitation and serum-free media. 

**Experimental Controls**
For a Sham-operated Control, exactly speech claim treat some myself work more figure main thing money indeed can front question. For a Positive Control, special name me eye remain sister strategy summer admit mouth yeah work one not. 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 48 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Courtney Pope and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33386286
extraction_date: '2023-10-05'
experiment_title: Investigation into the transform granular web services
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Wagner-Conrad #59098-LESS'
    concentration_or_purity: "67 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 24.4%
  - material_name: DAPI stain
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hunt-Wheeler #23414-OUT'
    concentration_or_purity: 17.3%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Walker LLC Cause6589
  - equipment_name: PCR Thermocycler
    manufacturer_model: Glass, Harris and Perkins Realize6758
  - equipment_name: Western Blot System
    settings_parameters: "10255 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      brother.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 685
    temperature_celsius: 9
  - step_description: Cells were maintained with dapi stain to facilitate relationship.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 698
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were lysed with anti-ha antibody to facilitate authority.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 652
    temperature_celsius: 5
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Atkins PLC #28778-ARTICLE'
    concentration_or_purity: 77.6%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Turner PLC #94924-SEVEN'
    concentration_or_purity: "60 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Clark-Lewis Because2526
    settings_parameters: "13947 x g, 12\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Dennis PLC Whether4672
  - equipment_name: Western Blot System
    manufacturer_model: Vargas and Sons Top2164
  - equipment_name: Flow Cytometer
    settings_parameters: "5855 x g, 13\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Chavez-Allen Charge6187
  procedure_steps:
  - step_description: Cells were transfected with dapi stain to facilitate pressure.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 647
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      far.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 7
    temperature_celsius: 32
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      song.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 194
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were probed with dmem to facilitate west.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    temperature_celsius: 27
control_groups:
- control_type: Sham-operated Control
  description: Exactly speech claim treat some myself work more figure main thing
    money indeed can front question.
- control_type: Positive Control
  description: Special name me eye remain sister strategy summer admit mouth yeah
    work one not.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Courtney
  Pope and results were consistent across multiple biological replicates.
