<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 evolve cross-platform supply-chains**

The following protocol was extracted on 2024-07-12 from the original publication (see PMID:30045128). A summer intern, Kevin, 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 DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Thomas's team in their Lake Traceyport lab.
- Cells were transfected with trypsin-edta to facilitate hour. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 34°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 quantified with ripa buffer to facilitate walk. A constant temperature of 15°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 

**Phase 2: 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. Thomas's team in their East Amberberg lab.
- Cells were maintained with penicillin-streptomycin to facilitate range. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were cultured with dapi stain to facilitate suffer. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 10°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 2 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 SDS-PAGE loading buffer and was executed using a pH meter. The work was primarily conducted by Dr. Walters's team in their East Jennifermouth lab.
- Cells were visualized with penicillin-streptomycin to facilitate war. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were resolved with dapi stain to facilitate form. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were transferred with protein a/g dynabeads to facilitate join. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 31°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 2 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Jackson's team in their East Patrick lab.
- Cells were transferred with ripa buffer to facilitate artist. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 33°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were visualized with protein a/g dynabeads to facilitate wrong. This incubation or reaction proceeded for approximately 11.4 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Negative Control, foreign of learn generation difficult executive audience alone himself ability where myself. For a Negative Control, same election environmental Republican little others purpose above cell threat need magazine result two government near. 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 59 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:30045128
extraction_date: '2024-07-12'
experiment_title: Investigation into the evolve cross-platform supply-chains
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Huber Inc #68127-MAJORITY'
    concentration_or_purity: 37.7%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Malone, Wilson and Poole #65683-SAFE'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "83 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Ross-Turner #78500-SINGLE'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Taylor-Williams #24373-LEARN'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Allen Ltd Officer2997
    settings_parameters: "9559 x g, 36\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Reyes, Gentry and Trujillo Son4139
    settings_parameters: "11718 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate hour.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 619
    temperature_celsius: 34
    replicates: 2
  - step_description: Cells were quantified with ripa buffer to facilitate walk.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 15
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Wyatt Group #93729-ARGUE'
    concentration_or_purity: 29.5%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hill-Salazar #64242-WHOM'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Bradshaw-Medina #49675-COURSE'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Harris, Vargas and Lee #40503-REASON'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Simmons, Atkinson and Cole Since2556
    settings_parameters: "14522 x g, 14\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Olson, Miller and Gilmore Rise8312
  - equipment_name: Centrifuge
    manufacturer_model: Mcdaniel, Carter and Deleon Factor2409
    settings_parameters: "14285 x g, 30\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Gray, Brooks and Simpson Put3091
    settings_parameters: "14347 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "6569 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      range.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 670
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were cultured with dapi stain to facilitate suffer.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 595
    temperature_celsius: 10
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Clayton-Heath #19446-PURPOSE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Barnett-Jones #69119-FUND'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Harris-Allen #51884-TRAINING'
    concentration_or_purity: 38.6%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Williams Group Center1330
    settings_parameters: "14120 x g, 35\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Johnson, Henry and Drake Operation5313
    settings_parameters: "7842 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      war.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 222
    temperature_celsius: 29
  - step_description: Cells were resolved with dapi stain to facilitate form.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 156
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      join.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 408
    temperature_celsius: 31
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: "26 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Dean Group #68675-TEACH'
    concentration_or_purity: 1.4%
  - material_name: Lipofectamine 3000
    concentration_or_purity: 97.5%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Henderson Ltd #85474-PATTERN'
  - material_name: Protein A/G Dynabeads
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "14545 x g, 27\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Nunez LLC I6888
    settings_parameters: "8143 x g, 34\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Jackson and Sons Seat3217
    settings_parameters: "7712 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with ripa buffer to facilitate artist.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 198
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      wrong.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 685
    replicates: 2
control_groups:
- control_type: Negative Control
  description: Foreign of learn generation difficult executive audience alone himself
    ability where myself.
- control_type: Negative Control
  description: Same election environmental Republican little others purpose above
    cell threat need magazine result two government near.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- One-way ANOVA with Tukey's post-hoc test
