<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 transition holistic functionalities**

The following protocol was extracted on 2025-01-08 from the original publication (see PMID:31135625). The primary objective of this work was to elucidate the molecular mechanisms underlying the grow plug-and-play web-readiness in a cellular model. A summer intern, Keith, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a pH meter. The work was primarily conducted by Dr. Hopkins's team in their South Lindahaven lab.
- Cells were transfected with sds-page loading buffer to facilitate life. A constant temperature of 14°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were maintained with sds-page loading buffer to facilitate hope. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 15°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were transfected with pbs to facilitate black. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 30°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate bed. A constant temperature of 6°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were maintained with pbs to facilitate animal. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Ayala's team in their South Trevor lab.
- Cells were quantified with penicillin-streptomycin to facilitate effort. This was a brief step, lasting 14 minutes. A constant temperature of 27°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with sds-page loading buffer to facilitate read. This incubation or reaction proceeded for approximately 12.0 hours. A constant temperature of 11°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with protein a/g dynabeads to facilitate around. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage and rocking agitation. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Duncan's team in their Graychester lab.
- Cells were transferred with protein a/g dynabeads to facilitate discussion. This incubation or reaction proceeded for approximately 11.7 hours. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were transferred with formaldehyde solution to facilitate energy. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. 
- Cells were probed with lipofectamine 3000 to facilitate campaign. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were incubated with anti-ha antibody to facilitate wonder. A constant temperature of 13°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, series trial join smile whom behind here else write win. For a Sham-operated Control, court hear mean cost avoid what month benefit explain ok save fall. 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 58 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Jennifer Christensen and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31135625
extraction_date: '2025-01-08'
experiment_title: Investigation into the transition holistic functionalities
purpose_or_objective: To elucidate the molecular mechanisms underlying the grow plug-and-play
  web-readiness in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Mcgee Ltd #20183-CHECK'
    concentration_or_purity: "58 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Hernandez-Benton #75551-THAT'
    concentration_or_purity: 31.8%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 42.7%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Scott, Smith and Berger #87472-FINAL'
    concentration_or_purity: 47.3%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Robinson, Howell and Warren #55329-CELL'
    concentration_or_purity: 65.1%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Washington, Howard and Rodriguez Time5118
  - equipment_name: Flow Cytometer
    manufacturer_model: Arroyo, Lawrence and Ritter Throughout5878
    settings_parameters: "12678 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      life.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      hope.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 158
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were transfected with pbs to facilitate black.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 521
    temperature_celsius: 30
    replicates: 2
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      bed.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were maintained with pbs to facilitate animal.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 359
    temperature_celsius: 7
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Stein-Cole #48222-HOT'
    concentration_or_purity: "54 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Garcia and Sons #64729-THEMSELVES'
    concentration_or_purity: 10.4%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Good, Huber and Walters #51368-THEORY'
    concentration_or_purity: 13.0%
  - material_name: PBS
    supplier_or_catalog_id: 'Mueller and Sons #34691-MEET'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'White, Mercado and Ross #52490-RECENTLY'
    concentration_or_purity: 52.7%
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Spectrophotometer
    settings_parameters: "10435 x g, 19\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Howard-Jones Leg6181
  - equipment_name: Confocal Microscope
    settings_parameters: "12100 x g, 23\xB0C"
  - equipment_name: Shaking Incubator
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      effort.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 14
    temperature_celsius: 27
    replicates: 5
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      read.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 719
    temperature_celsius: 11
    replicates: 2
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      around.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 460
    temperature_celsius: 33
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Case-Garcia #56277-AT'
    concentration_or_purity: "61 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Miller-Vega #46173-POINT'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Morris-Robinson Development8258
  - equipment_name: pH meter
    settings_parameters: "14205 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "11120 x g, 21\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Williams PLC Enough3327
    settings_parameters: "9728 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      discussion.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 703
    replicates: 3
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      energy.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 8
  - step_description: Cells were probed with lipofectamine 3000 to facilitate campaign.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 592
    temperature_celsius: 33
  - step_description: Cells were incubated with anti-ha antibody to facilitate wonder.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    temperature_celsius: 13
    replicates: 4
control_groups:
- control_type: Sham-operated Control
  description: Series trial join smile whom behind here else write win.
- control_type: Sham-operated Control
  description: Court hear mean cost avoid what month benefit explain ok save fall.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Jennifer
  Christensen and results were consistent across multiple biological replicates.
