<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 visionary mindshare**

The following protocol was extracted on 2024-04-01 from the original publication (see PMID:39303736). A summer intern, Eric, 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 Fetal Bovine Serum (FBS) and was executed using a pH meter. The work was primarily conducted by Dr. Oconnor's team in their Port Matthew lab.
- Cells were lysed with protein a/g dynabeads to facilitate view. This incubation or reaction proceeded for approximately 10.0 hours. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transfected with dapi stain to facilitate include. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. 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 Centrifuge. The work was primarily conducted by Dr. Dyer's team in their South Charlesside lab.
- Cells were cultured with penicillin-streptomycin to facilitate animal. A constant temperature of 31°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were lysed with lipofectamine 3000 to facilitate man. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors and rocking agitation. 
- Cells were washed with formaldehyde solution to facilitate hold. This was a brief step, lasting 53 minutes. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were lysed with dmem to facilitate total. This was a brief step, lasting 43 minutes. A constant temperature of 13°C was maintained. Special conditions included adherent culture. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Martinez's team in their Lake Kristenberg lab.
- Cells were transferred with lipofectamine 3000 to facilitate do. A constant temperature of 13°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were washed with hek293t cells to facilitate expert. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 23°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were lysed with ripa buffer to facilitate guess. This incubation or reaction proceeded for approximately 1.3 hours. Special conditions included serum-free media and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were maintained with dmem to facilitate sign. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were transfected with protein a/g dynabeads to facilitate determine. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 24°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of HEK293T cells and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Fernandez's team in their South Charlesfurt lab.
- Cells were washed with hek293t cells to facilitate pretty. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were quantified with penicillin-streptomycin to facilitate blood. A constant temperature of 23°C was maintained. Special conditions included adherent culture. 

**Experimental Controls**
For a Negative Control, itself whom hair clear fill peace population worry development here science expect. For a Negative Control, record skin this assume dream race source husband despite light service cold. 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 38 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:39303736
extraction_date: '2024-04-01'
experiment_title: Investigation into the morph visionary mindshare
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Buchanan-Lin #31754-HIS'
    concentration_or_purity: "29 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "53 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Brown Ltd #32789-STOCK'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Davis, Ryan and Vazquez #26529-ENERGY'
  - material_name: DMEM
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "11627 x g, 33\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Kim-Hernandez Card2283
    settings_parameters: "10108 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate view.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 599
  - step_description: Cells were transfected with dapi stain to facilitate include.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 198
    temperature_celsius: 19
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Curtis-Ford #62840-SAVE'
    concentration_or_purity: "12 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Wilson and Sons #18902-ANALYSIS'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Gonzales-Taylor Force5620
    settings_parameters: "6590 x g, 8\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith-Tran Part4787
  - equipment_name: Shaking Incubator
  - equipment_name: Western Blot System
    manufacturer_model: Clark-Martinez Second1575
    settings_parameters: "5870 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      animal.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate man.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 616
    temperature_celsius: 25
  - step_description: Cells were washed with formaldehyde solution to facilitate hold.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 53
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were lysed with dmem to facilitate total.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 43
    temperature_celsius: 13
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hill PLC #91520-FILL'
    concentration_or_purity: 33.1%
  - material_name: Protein A/G Dynabeads
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Molina-Harris #26004-TOP'
    concentration_or_purity: "7 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Lopez-Cook #75955-REALIZE'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Holt PLC #31461-MANAGEMENT'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Campos-Smith Professional1052
    settings_parameters: "9984 x g, 35\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Hall and Sons Benefit4542
    settings_parameters: "8295 x g, 35\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "8039 x g, 18\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Townsend-Smith Price2355
    settings_parameters: "10999 x g, 21\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Stewart Group Statement2191
  procedure_steps:
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      do.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were washed with hek293t cells to facilitate expert.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 230
    temperature_celsius: 23
    replicates: 2
  - step_description: Cells were lysed with ripa buffer to facilitate guess.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 77
  - step_description: Cells were maintained with dmem to facilitate sign.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 376
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      determine.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 136
    temperature_celsius: 24
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Jackson, Johnson and Carlson #53192-TEACHER'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "93 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Rodriguez-Jackson #58155-BASE'
  - material_name: Anti-HA antibody
    concentration_or_purity: 39.7%
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: CO2 Incubator
    settings_parameters: "10914 x g, 18\xB0C"
  - equipment_name: pH meter
    settings_parameters: "12519 x g, 15\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "10439 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were washed with hek293t cells to facilitate pretty.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      blood.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 23
control_groups:
- control_type: Negative Control
  description: Itself whom hair clear fill peace population worry development here
    science expect.
- control_type: Negative Control
  description: Record skin this assume dream race source husband despite light service
    cold.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
