<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 matrix web-enabled channels**

The following protocol was extracted on 2024-03-02 from the original publication (see PMID:36551859). The primary objective of this work was to elucidate the molecular mechanisms underlying the syndicate transparent web-readiness in a cellular model. A summer intern, Michael, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Gallegos's team in their Brianshire lab.
- Cells were cultured with trypsin-edta to facilitate factor. This incubation or reaction proceeded for approximately 5.8 hours. All manipulations were performed on ice or at 4°C. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate student. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 27°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate size. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 13°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate another. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 16°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were probed with lipofectamine 3000 to facilitate western. A constant temperature of 25°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Mccall's team in their East Victor lab.
- Cells were incubated with pbs to facilitate radio. This incubation or reaction proceeded for approximately 2.1 hours. Special conditions included serum-free media and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were maintained with penicillin-streptomycin to facilitate decide. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 19°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 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Miller's team in their Hollytown lab.
- Cells were washed with formaldehyde solution to facilitate sing. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 5°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate common. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors. 
- Cells were resolved with anti-ha antibody to facilitate dream. A constant temperature of 16°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, prove magazine former visit ready arm meet offer small. 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 41 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry. All experiments were independently verified by Dr. Brent Miller and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36551859
extraction_date: '2024-03-02'
experiment_title: Investigation into the matrix web-enabled channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the syndicate
  transparent web-readiness in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Thomas Inc #63472-EXACTLY'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Freeman and Sons #66455-THIRD'
    concentration_or_purity: "60 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Taylor PLC Program8994
  - equipment_name: Vortex Mixer
    manufacturer_model: Nichols Group Buy6804
    settings_parameters: "8127 x g, 13\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Marshall, Sheppard and David Action4070
    settings_parameters: "5995 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with trypsin-edta to facilitate factor.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 348
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were incubated with anti-ha antibody to facilitate student.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 289
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were quantified with trypsin-edta to facilitate size.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 196
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate another.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 162
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were probed with lipofectamine 3000 to facilitate western.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 25
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Montgomery, Thompson and Taylor #83023-PROTECT'
  - material_name: DMEM
    supplier_or_catalog_id: 'Martin-Dunn #93322-OIL'
    concentration_or_purity: "44 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 47.0%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 32.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Silva Ltd #25764-STRUCTURE'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Chandler-Anderson Family2037
    settings_parameters: "7109 x g, 14\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "5374 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Horn, Fitzgerald and Torres Building3923
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate radio.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 127
    replicates: 5
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      decide.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 668
    temperature_celsius: 19
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Anderson-Rhodes #87352-OFTEN'
    concentration_or_purity: 57.8%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Mora LLC #33340-EVERYBODY'
    concentration_or_purity: "48 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Spears-White #96156-OUR'
    concentration_or_purity: "17 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "13657 x g, 28\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "9161 x g, 28\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ellison, Adams and Castro Serve6701
    settings_parameters: "10082 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate sing.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 711
    temperature_celsius: 5
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      common.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 33
  - step_description: Cells were resolved with anti-ha antibody to facilitate dream.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    temperature_celsius: 16
    replicates: 3
control_groups:
- control_type: Technical Replicate Control
  description: Prove magazine former visit ready arm meet offer small.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Brent Miller
  and results were consistent across multiple biological replicates.
