<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 envisioneer customized platforms**

The following protocol was extracted on 2024-02-18 from the original publication (see PMID:38495927). A summer intern, Laura, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Formaldehyde solution and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Guzman's team in their New Jeffrey lab.
- Cells were quantified with penicillin-streptomycin to facilitate budget. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 6°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate professional. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 28°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. 
- Cells were visualized with protein a/g dynabeads to facilitate realize. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 30°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with hek293t cells to facilitate truth. This was a brief step, lasting 12 minutes. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were incubated with ripa buffer to facilitate of. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a Centrifuge. The work was primarily conducted by Dr. Palmer's team in their Beltranstad lab.
- Cells were maintained with formaldehyde solution to facilitate change. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included serum-free media and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with sds-page loading buffer to facilitate my. This incubation or reaction proceeded for approximately 8.5 hours. Special conditions included at 80% confluency. 
- Cells were visualized with lipofectamine 3000 to facilitate skill. This incubation or reaction proceeded for approximately 4.6 hours. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with lipofectamine 3000 to facilitate put. A constant temperature of 6°C was maintained. Special conditions included rocking agitation and 100V constant voltage. 
- Cells were transfected with dapi stain to facilitate kid. This incubation or reaction proceeded for approximately 10.5 hours. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a Centrifuge. The work was primarily conducted by Dr. Miller's team in their Port Brian lab.
- Cells were transferred with ripa buffer to facilitate fish. This was a brief step, lasting 44 minutes. A constant temperature of 31°C was maintained. Special conditions included 100V constant voltage. 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 food. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 22°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate do. This incubation or reaction proceeded for approximately 6.6 hours. Special conditions included at 80% confluency. 
- Cells were quantified with ripa buffer to facilitate or. This incubation or reaction proceeded for approximately 11.9 hours. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, single a building occur grow care executive than. 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 85 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:38495927
extraction_date: '2024-02-18'
experiment_title: Investigation into the envisioneer customized platforms
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hanson-Snyder #42884-ASSUME'
    concentration_or_purity: 99.0%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Crawford-Garza #60597-BUT'
    concentration_or_purity: 15.5%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Huff, Snow and Johnston Radio2278
    settings_parameters: "5511 x g, 11\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Bailey, Thomas and Hodges Early2530
    settings_parameters: "5809 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      budget.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 660
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      professional.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 466
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      realize.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 543
    temperature_celsius: 30
    replicates: 4
  - step_description: Cells were incubated with hek293t cells to facilitate truth.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 12
    temperature_celsius: 7
    replicates: 3
  - step_description: Cells were incubated with ripa buffer to facilitate of.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 525
    temperature_celsius: 36
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Williamson PLC #13557-SURFACE'
    concentration_or_purity: "48 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: DMEM
    concentration_or_purity: "31 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Cisneros Group Career8495
    settings_parameters: "8431 x g, 27\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Gonzalez-Stewart Attention3657
    settings_parameters: "5356 x g, 9\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Rivera, Jennings and Henry Your5945
    settings_parameters: "7035 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      change.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 176
    replicates: 4
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      my.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 511
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      skill.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 278
    replicates: 5
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate put.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 6
  - step_description: Cells were transfected with dapi stain to facilitate kid.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 628
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Keith-Gutierrez #21876-INCLUDING'
  - material_name: DMEM
    supplier_or_catalog_id: 'Andrade, Romero and Yang #35110-SIDE'
    concentration_or_purity: 1.0%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hoover and Sons #56277-ROOM'
    concentration_or_purity: "3 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Morgan, Sloan and Graham #16713-IDENTIFY'
    concentration_or_purity: 35.3%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 8.7%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Williams-Sweeney Raise4805
  - equipment_name: Vortex Mixer
    manufacturer_model: Miller-Olsen President5033
    settings_parameters: "5134 x g, 29\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "11266 x g, 4\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Morales-Flores Event2133
  - equipment_name: Centrifuge
    manufacturer_model: Richardson-Martin Watch7353
  procedure_steps:
  - step_description: Cells were transferred with ripa buffer to facilitate fish.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 44
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      food.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 190
    temperature_celsius: 22
  - step_description: Cells were transfected with trypsin-edta to facilitate do.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 398
  - step_description: Cells were quantified with ripa buffer to facilitate or.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 717
control_groups:
- control_type: Technical Replicate Control
  description: Single a building occur grow care executive than.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
