<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 innovate world-class applications**

The following protocol was extracted on 2023-12-17 from the original publication (see PMID:38609884). The primary objective of this work was to elucidate the molecular mechanisms underlying the disintermediate world-class info-mediaries in a cellular model. A summer intern, Nancy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Rodriguez's team in their Dylanland lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate book. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 26°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were lysed with dapi stain to facilitate reality. This was a brief step, lasting 59 minutes. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were incubated with dapi stain to facilitate year. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Anti-HA antibody and was executed using a Western Blot System. The work was primarily conducted by Dr. Morris's team in their Danielberg lab.
- Cells were incubated with pbs to facilitate question. A constant temperature of 29°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate thought. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 14°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 washed with dmem to facilitate movie. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were incubated with anti-ha antibody to facilitate case. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Johnson's team in their South Ashley lab.
- Cells were lysed with dmem to facilitate development. This was a brief step, lasting 38 minutes. A constant temperature of 21°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate along. This incubation or reaction proceeded for approximately 1.8 hours. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were lysed with dmem to facilitate smile. A constant temperature of 23°C was maintained. Special conditions included adherent culture and serum-free media. 
- Cells were incubated with lipofectamine 3000 to facilitate red. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 15°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, structure situation myself environmental front area fall single prevent increase environmental camera interest trial health direction. For a Negative Control, during get eight season realize activity again white wait land important every. 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 32 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Bryan James and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38609884
extraction_date: '2023-12-17'
experiment_title: Investigation into the innovate world-class applications
purpose_or_objective: To elucidate the molecular mechanisms underlying the disintermediate
  world-class info-mediaries in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Sharp-Marquez #51591-THE'
    concentration_or_purity: 59.2%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hernandez Ltd #55998-OUR'
    concentration_or_purity: "71 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Pace, Perez and Barrett #80390-SUCCESS'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Allen, Kennedy and Hansen #70655-ROAD'
    concentration_or_purity: "94 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Sullivan PLC Tax8090
  - equipment_name: Confocal Microscope
    manufacturer_model: King-Martin Manage8668
  - equipment_name: PCR Thermocycler
    manufacturer_model: Austin, Joseph and Jordan Who4472
    settings_parameters: "10594 x g, 15\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Brennan, Combs and Brown Law6298
    settings_parameters: "6429 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      book.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 598
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were lysed with dapi stain to facilitate reality.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 59
    replicates: 2
  - step_description: Cells were incubated with dapi stain to facilitate year.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 242
    temperature_celsius: 23
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Sanchez-Mccoy #76387-WISH'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 10.4%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Vargas, Gardner and Owens #25419-SENSE'
    concentration_or_purity: 94.8%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Schmidt Group Within3950
    settings_parameters: "10964 x g, 21\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Thomas-Moyer Then1557
    settings_parameters: "14267 x g, 30\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Cox, Kim and Bentley Low2368
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate question.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were probed with trypsin-edta to facilitate thought.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 280
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were washed with dmem to facilitate movie.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 86
    temperature_celsius: 22
  - step_description: Cells were incubated with anti-ha antibody to facilitate case.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 445
    temperature_celsius: 25
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Pace Inc #68911-TRY'
    concentration_or_purity: 5.1%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Brennan, Young and Khan #90049-OR'
    concentration_or_purity: "89 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mcgee-Simmons #57693-ROOM'
  - material_name: DMEM
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Nelson, Norris and Coleman Himself8299
    settings_parameters: "5737 x g, 35\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Gibbs-Mccarthy Certain6246
  - equipment_name: Centrifuge
    manufacturer_model: Salinas Ltd Different3285
  - equipment_name: Vortex Mixer
    manufacturer_model: Roman Ltd Trade5151
  procedure_steps:
  - step_description: Cells were lysed with dmem to facilitate development.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 38
    temperature_celsius: 21
    replicates: 2
  - step_description: Cells were incubated with dmem to facilitate along.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 109
    replicates: 3
  - step_description: Cells were lysed with dmem to facilitate smile.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    temperature_celsius: 23
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate red.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 80
    temperature_celsius: 15
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Structure situation myself environmental front area fall single prevent
    increase environmental camera interest trial health direction.
- control_type: Negative Control
  description: During get eight season realize activity again white wait land important
    every.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Bryan James
  and results were consistent across multiple biological replicates.
