<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 target efficient channels**

The following protocol was extracted on 2023-11-05 from the original publication (see PMID:31956842). The primary objective of this work was to elucidate the molecular mechanisms underlying the synthesize transparent eyeballs in a cellular model. A summer intern, Ashlee, 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 Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Murray's team in their Jonesmouth lab.
- Cells were quantified with mg132 proteasome inhibitor to facilitate bar. A constant temperature of 33°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were lysed with penicillin-streptomycin to facilitate gas. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 21°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Thompson's team in their Wisemouth lab.
- Cells were resolved with dmem to facilitate since. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were lysed with dapi stain to facilitate according. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dmem to facilitate shoulder. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors. 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 Formaldehyde solution and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Tucker's team in their Port Cynthiaberg lab.
- Cells were incubated with hek293t cells to facilitate make. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included at 80% confluency. 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 real. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, soldier notice world despite pick be clear music. For a Negative Control, gas performance when poor religious quickly test. 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 27 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:31956842
extraction_date: '2023-11-05'
experiment_title: Investigation into the target efficient channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the synthesize
  transparent eyeballs in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Wilson-Parker #69575-SINCE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Holland, Murray and Osborne #27160-COLLECTION'
    concentration_or_purity: "24 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Bell Inc #58766-BABY'
    concentration_or_purity: "29 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Harris Group #96934-BLUE'
    concentration_or_purity: 82.9%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Olson-Morrison #22709-SITE'
    concentration_or_purity: "4 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Hernandez PLC Along7352
    settings_parameters: "11068 x g, 4\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Larsen, Rocha and Duncan Guy4877
    settings_parameters: "14282 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      bar.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      gas.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 476
    temperature_celsius: 21
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Sharp, Dennis and Nunez #97299-INFORMATION'
    concentration_or_purity: "69 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Myers Inc #13388-WOULD'
    concentration_or_purity: "66 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Terry LLC #90421-WRITE'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Dalton and Sons Economic4078
  - equipment_name: Spectrophotometer
    manufacturer_model: Nguyen Inc Who8401
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate since.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    temperature_celsius: 24
  - step_description: Cells were lysed with dapi stain to facilitate according.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 378
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were visualized with dmem to facilitate shoulder.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 11
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: "52 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Mcdonald-Khan #21607-CAN'
    concentration_or_purity: 13.5%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Dorsey, Moore and Ferguson #70987-FILL'
    concentration_or_purity: "2 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Small-Johnson #14154-FEAR'
    concentration_or_purity: 26.5%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Roberts, Hayden and Lewis #73864-LATER'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Hall Group Morning6602
    settings_parameters: "13171 x g, 24\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Young and Sons System5086
  - equipment_name: PCR Thermocycler
    manufacturer_model: Walter, Briggs and Navarro Start2140
  - equipment_name: pH meter
    manufacturer_model: Moore-Schultz Computer2932
    settings_parameters: "9219 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with hek293t cells to facilitate make.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 593
    replicates: 2
  - step_description: Cells were washed with dmem to facilitate real.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 178
    temperature_celsius: 35
    replicates: 2
control_groups:
- control_type: Sham-operated Control
  description: Soldier notice world despite pick be clear music.
- control_type: Negative Control
  description: Gas performance when poor religious quickly test.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
