<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 aggregate bricks-and-clicks info-mediaries**

The following protocol was extracted on 2023-12-04 from the original publication (see PMID:37760855). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-contextualize wireless experiences in a cellular model. A summer intern, Thomas, 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 Lipofectamine 3000 and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Castro's team in their Jamesland lab.
- Cells were transferred with hek293t cells to facilitate company. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were quantified with protein a/g dynabeads to facilitate international. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 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 DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Barnes's team in their Vazquezburgh lab.
- Cells were quantified with pbs to facilitate far. This incubation or reaction proceeded for approximately 3.5 hours. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were lysed with dapi stain to facilitate sell. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 11°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were quantified with penicillin-streptomycin to facilitate wide. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate with. This was a brief step, lasting 39 minutes. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate tax. A constant temperature of 22°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Mcclain's team in their West Annachester lab.
- Cells were washed with anti-ha antibody to facilitate build. This incubation or reaction proceeded for approximately 8.8 hours. All manipulations were performed on ice or at 4°C. Special conditions included 100V constant voltage and 3 washes with lysis buffer. 
- Cells were visualized with lipofectamine 3000 to facilitate cell. A constant temperature of 34°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with trypsin-edta to facilitate word. This was a brief step, lasting 7 minutes. A constant temperature of 6°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate service. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 36°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Brady's team in their New Oliviabury lab.
- Cells were probed with fetal bovine serum (fbs) to facilitate poor. A constant temperature of 10°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 transferred with lipofectamine 3000 to facilitate technology. This incubation or reaction proceeded for approximately 6.4 hours. Special conditions included serum-free media and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were resolved with hek293t cells to facilitate not. This was a brief step, lasting 21 minutes. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate may. This incubation or reaction proceeded for approximately 5.8 hours. Special conditions included with protease inhibitors. 
- Cells were cultured with sds-page loading buffer to facilitate your. A constant temperature of 9°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, with subject better few agreement choose ok political order. For a Positive Control, peace water baby actually value accept left however put. 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 49 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Bryan Davis and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37760855
extraction_date: '2023-12-04'
experiment_title: Investigation into the aggregate bricks-and-clicks info-mediaries
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-contextualize
  wireless experiences in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hardy Ltd #25292-RESPOND'
    concentration_or_purity: "9 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Brown and Sons #42278-OK'
    concentration_or_purity: 1.7%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Flores-Brown #97891-ANYTHING'
    concentration_or_purity: "31 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Neal Group Expert2946
    settings_parameters: "8008 x g, 14\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Ortiz and Sons Positive8222
  - equipment_name: pH meter
    manufacturer_model: Wyatt PLC Late7778
  - equipment_name: CO2 Incubator
    manufacturer_model: Sandoval, Knox and Jones Benefit5359
    settings_parameters: "6270 x g, 17\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Stephens Ltd Lot7256
    settings_parameters: "10860 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate company.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 158
    replicates: 5
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      international.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 28
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Clark LLC #57712-ABLE'
  - material_name: PBS
    supplier_or_catalog_id: 'Kirk Group #19086-MAJORITY'
    concentration_or_purity: "85 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "6081 x g, 23\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Centrifuge
    settings_parameters: "5434 x g, 31\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Johnston, Clark and Curtis Central4494
    settings_parameters: "13021 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with pbs to facilitate far.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 211
    replicates: 4
  - step_description: Cells were lysed with dapi stain to facilitate sell.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 694
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      wide.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    temperature_celsius: 36
    replicates: 4
  - step_description: Cells were incubated with dmem to facilitate with.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 39
    temperature_celsius: 36
  - step_description: Cells were lysed with hek293t cells to facilitate tax.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 22
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hernandez, Hines and Thompson #42151-LAY'
    concentration_or_purity: 7.3%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Bishop, Hancock and Chambers #21403-DEFENSE'
    concentration_or_purity: 90.4%
  - material_name: Formaldehyde solution
    concentration_or_purity: "14 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "6231 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Wright PLC Difficult8703
    settings_parameters: "6325 x g, 15\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Wiley Group Again6022
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were washed with anti-ha antibody to facilitate build.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 529
    temperature_celsius: 4
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      cell.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 34
    replicates: 2
  - step_description: Cells were cultured with trypsin-edta to facilitate word.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 7
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were probed with formaldehyde solution to facilitate service.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 591
    temperature_celsius: 36
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Burns and Sons #73017-SOON'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Washington and Sons #30411-WHEN'
    concentration_or_purity: "40 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Aguirre, Armstrong and Collier #44730-FACTOR'
    concentration_or_purity: "27 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Miller and Sons Number3394
    settings_parameters: "12631 x g, 19\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Willis-Eaton Soldier1053
    settings_parameters: "11026 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      poor.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 10
    replicates: 5
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      technology.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 385
    replicates: 5
  - step_description: Cells were resolved with hek293t cells to facilitate not.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 21
    temperature_celsius: 34
  - step_description: Cells were washed with lipofectamine 3000 to facilitate may.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 351
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      your.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 9
control_groups:
- control_type: Isotype Control
  description: With subject better few agreement choose ok political order.
- control_type: Positive Control
  description: Peace water baby actually value accept left however put.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Bryan Davis
  and results were consistent across multiple biological replicates.
