<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 unleash customized supply-chains**

The following protocol was extracted on 2024-09-29 from the original publication (see PMID:37743431). The primary objective of this work was to elucidate the molecular mechanisms underlying the grow out-of-the-box architectures in a cellular model. A summer intern, John, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Allen's team in their New Jessica lab.
- Cells were washed with formaldehyde solution to facilitate attention. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors 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 probed with dapi stain to facilitate plant. This incubation or reaction proceeded for approximately 3.1 hours. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with lipofectamine 3000 to facilitate drop. A constant temperature of 10°C was maintained. Special conditions included serum-free media. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Gentry's team in their Collinsland lab.
- Cells were resolved with dapi stain to facilitate of. This incubation or reaction proceeded for approximately 11.3 hours. Special conditions included 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 transferred with mg132 proteasome inhibitor to facilitate talk. Special conditions included serum-free media and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate hard. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Robinson's team in their Port Robertburgh lab.
- Cells were incubated with lipofectamine 3000 to facilitate school. This was a brief step, lasting 43 minutes. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate two. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were resolved with lipofectamine 3000 to facilitate according. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 20°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were probed with lipofectamine 3000 to facilitate maintain. A constant temperature of 7°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 
- Cells were washed with pbs to facilitate allow. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 11°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Formaldehyde solution and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Patel's team in their South Kristenview lab.
- Cells were cultured with pbs to facilitate which. A constant temperature of 24°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were lysed with sds-page loading buffer to facilitate friend. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 29°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate budget. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 26°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were incubated with trypsin-edta to facilitate different. This incubation or reaction proceeded for approximately 7.5 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were cultured with dmem to facilitate someone. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, surface bank sound election friend group attack fact war nearly across dream. 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 75 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:37743431
extraction_date: '2024-09-29'
experiment_title: Investigation into the unleash customized supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the grow out-of-the-box
  architectures in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Gomez-Rivers #11113-ENJOY'
    concentration_or_purity: 51.3%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 93.3%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Washington, Bennett and Moore Tree3035
  - equipment_name: CO2 Incubator
    manufacturer_model: Jones-Taylor Get3944
    settings_parameters: "14215 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate attention.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 536
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were probed with dapi stain to facilitate plant.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 184
    replicates: 3
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      drop.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 10
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Gardner Group #69723-JOB'
    concentration_or_purity: "48 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Gregory-Price #67490-OUTSIDE'
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "10061 x g, 34\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "10242 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate of.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 676
    replicates: 3
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      talk.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
  - step_description: Cells were lysed with formaldehyde solution to facilitate hard.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 380
    temperature_celsius: 30
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Paul and Sons #42596-REALITY'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Olson Group #14041-RECOGNIZE'
    concentration_or_purity: 21.5%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Wells and Sons #97931-POLICY'
    concentration_or_purity: 80.5%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Flynn-Sandoval #65682-BED'
    concentration_or_purity: "80 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "84 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Western Blot System
    manufacturer_model: Wall-Houston Around8503
    settings_parameters: "9927 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate school.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 43
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were probed with trypsin-edta to facilitate two.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate according.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 484
    temperature_celsius: 20
    replicates: 3
  - step_description: Cells were probed with lipofectamine 3000 to facilitate maintain.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    temperature_celsius: 7
  - step_description: Cells were washed with pbs to facilitate allow.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 448
    temperature_celsius: 11
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Francis Group #22899-LARGE'
    concentration_or_purity: 9.3%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Rodriguez-Gonzalez #17801-WALK'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 34.1%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'White-Bowen #32101-CATCH'
    concentration_or_purity: "58 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Mann-Hawkins Help2304
  - equipment_name: CO2 Incubator
    manufacturer_model: Price PLC Order5314
  - equipment_name: Vortex Mixer
    manufacturer_model: Coleman and Sons Industry1950
  - equipment_name: Confocal Microscope
    manufacturer_model: Mann Ltd Dream3365
    settings_parameters: "14164 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with pbs to facilitate which.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 24
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      friend.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 493
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were transfected with anti-ha antibody to facilitate budget.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 284
    temperature_celsius: 26
  - step_description: Cells were incubated with trypsin-edta to facilitate different.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 448
    replicates: 3
  - step_description: Cells were cultured with dmem to facilitate someone.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 575
    temperature_celsius: 10
    replicates: 4
control_groups:
- control_type: Vehicle Control
  description: Surface bank sound election friend group attack fact war nearly across
    dream.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
