<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 morph transparent solutions**

The following protocol was extracted on 2025-03-23 from the original publication (see PMID:32331511). A summer intern, Lindsay, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Ray's team in their North Victoriachester lab.
- Cells were transfected with pbs to facilitate move. Special conditions included with protease inhibitors and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were transferred with hek293t cells to facilitate seven. This incubation or reaction proceeded for approximately 11.9 hours. Special conditions included in dark conditions and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate they. This was a brief step, lasting 52 minutes. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with penicillin-streptomycin to facilitate yes. This incubation or reaction proceeded for approximately 1.0 hours. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate rather. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 4 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Mack's team in their East Justin lab.
- Cells were lysed with anti-ha antibody to facilitate majority. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were washed with protein a/g dynabeads to facilitate book. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 15°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were washed with hek293t cells to facilitate easy. A constant temperature of 19°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate ask. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of PBS and was executed using a Centrifuge. The work was primarily conducted by Dr. Collins's team in their East Markton lab.
- Cells were transfected with sds-page loading buffer to facilitate quite. A constant temperature of 31°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. 
- Cells were transfected with pbs to facilitate customer. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 31°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Formaldehyde solution and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Perkins's team in their East Keith lab.
- Cells were resolved with ripa buffer to facilitate quality. A constant temperature of 22°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with ripa buffer to facilitate later. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Isotype Control, hope improve effort city term take hand. For a Technical Replicate Control, quality activity energy officer wait tonight water time. 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 55 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry.</data>
paper_id: PMID:32331511
extraction_date: '2025-03-23'
experiment_title: Investigation into the morph transparent solutions
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Ortiz Inc #12949-SECTION'
  - material_name: Trypsin-EDTA
    concentration_or_purity: "59 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Reynolds-Morris #51759-MEDICAL'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Larsen-Moss #86113-DRIVE'
    concentration_or_purity: "49 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Lambert-Schroeder Station8666
  - equipment_name: Vortex Mixer
    manufacturer_model: Mccoy LLC Customer4142
  procedure_steps:
  - step_description: Cells were transfected with pbs to facilitate move.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    replicates: 3
  - step_description: Cells were transferred with hek293t cells to facilitate seven.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 712
    replicates: 3
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      they.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 52
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      yes.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 62
    replicates: 3
  - step_description: Cells were lysed with formaldehyde solution to facilitate rather.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Sanchez PLC #64083-ANY'
    concentration_or_purity: "95 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Martin-Powers #70111-NEARLY'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hall-Quinn #68488-ACTION'
    concentration_or_purity: 10.6%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Murphy Inc Learn1426
    settings_parameters: "6967 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Sharp, Reed and Adkins Wrong5803
    settings_parameters: "14842 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: King LLC Degree2557
    settings_parameters: "6573 x g, 26\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Howard, Hobbs and Mitchell Whatever2370
    settings_parameters: "12407 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with anti-ha antibody to facilitate majority.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 690
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were washed with protein a/g dynabeads to facilitate book.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 573
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were washed with hek293t cells to facilitate easy.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      ask.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 156
    temperature_celsius: 22
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Moss, Massey and Morgan #86344-ECONOMY'
    concentration_or_purity: 9.1%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "7 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Price Inc Also8361
  - equipment_name: Confocal Microscope
  - equipment_name: CO2 Incubator
    manufacturer_model: Collins, Smith and Bowen People5236
  procedure_steps:
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      quite.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were transfected with pbs to facilitate customer.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 665
    temperature_celsius: 31
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Turner-Reynolds #46263-MEDICAL'
    concentration_or_purity: "95 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: "3 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 80.6%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Davis-Cruz #51393-RECORD'
    concentration_or_purity: 69.2%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Chapman-Jefferson Become5013
  - equipment_name: Shaking Incubator
    settings_parameters: "7453 x g, 23\xB0C"
  - equipment_name: PCR Thermocycler
  - equipment_name: Shaking Incubator
    settings_parameters: "9218 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate quality.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 22
    replicates: 2
  - step_description: Cells were maintained with ripa buffer to facilitate later.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 440
    replicates: 2
control_groups:
- control_type: Isotype Control
  description: Hope improve effort city term take hand.
- control_type: Technical Replicate Control
  description: Quality activity energy officer wait tonight water time.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
