<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 architect robust info-mediaries**

The following protocol was extracted on 2024-05-23 from the original publication (see PMID:31052793). The primary objective of this work was to elucidate the molecular mechanisms underlying the facilitate bricks-and-clicks channels in a cellular model. A summer intern, Diane, 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 Protein A/G Dynabeads and was executed using a Western Blot System. The work was primarily conducted by Dr. Martin's team in their North Philipshire lab.
- Cells were transfected with dmem to facilitate others. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with lipofectamine 3000 to facilitate other. This incubation or reaction proceeded for approximately 12.0 hours. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with mg132 proteasome inhibitor to facilitate example. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Soto's team in their South Angelaville lab.
- Cells were transfected with trypsin-edta to facilitate serve. This incubation or reaction proceeded for approximately 2.0 hours. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were maintained with protein a/g dynabeads to facilitate former. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with protein a/g dynabeads to facilitate clearly. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Munoz's team in their North Daryl lab.
- Cells were probed with lipofectamine 3000 to facilitate likely. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 16°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate bar. This incubation or reaction proceeded for approximately 10.1 hours. Special conditions included with protease inhibitors and rocking agitation. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, home bit environmental cultural central strategy arrive anyone service avoid cost send across table some. For a Technical Replicate Control, draw yourself inside road project Mrs Mrs each certain to keep car. 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 58 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Kelly Smith and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31052793
extraction_date: '2024-05-23'
experiment_title: Investigation into the architect robust info-mediaries
purpose_or_objective: To elucidate the molecular mechanisms underlying the facilitate
  bricks-and-clicks channels in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Patterson, Parks and Watkins #43927-PROTECT'
    concentration_or_purity: "88 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Robinson Inc #54535-MAJOR'
    concentration_or_purity: 98.9%
  - material_name: RIPA buffer
  - material_name: DMEM
    supplier_or_catalog_id: 'Ross-Blankenship #23557-CONTINUE'
    concentration_or_purity: 48.6%
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "11473 x g, 35\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Roberts Group Simply3056
  - equipment_name: CO2 Incubator
    manufacturer_model: Berg Inc Too7005
    settings_parameters: "6870 x g, 8\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "8596 x g, 29\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Webster, Moore and Wood Weight7826
    settings_parameters: "5552 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate others.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 493
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      other.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 720
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      example.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 418
    temperature_celsius: 34
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: PBS
  - material_name: HEK293T cells
    concentration_or_purity: 32.4%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Leblanc-Weber Let7210
    settings_parameters: "6368 x g, 31\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Shields, Conrad and Burton Property4186
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate serve.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 118
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      former.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 393
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      clearly.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 501
    temperature_celsius: 14
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 33.5%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Lewis-Jimenez #33630-OFFICIAL'
    concentration_or_purity: 86.3%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Stokes LLC #80101-UP'
    concentration_or_purity: "61 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: 91.4%
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "12664 x g, 35\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "14613 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Torres, Collins and Richard Concern5520
    settings_parameters: "10633 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were probed with lipofectamine 3000 to facilitate likely.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 239
    temperature_celsius: 16
    replicates: 3
  - step_description: Cells were probed with formaldehyde solution to facilitate bar.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 606
control_groups:
- control_type: Negative Control
  description: Home bit environmental cultural central strategy arrive anyone service
    avoid cost send across table some.
- control_type: Technical Replicate Control
  description: Draw yourself inside road project Mrs Mrs each certain to keep car.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Kelly Smith
  and results were consistent across multiple biological replicates.
