<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 24/7 deliverables**

The following protocol was extracted on 2025-06-18 from the original publication (see PMID:34389490). The primary objective of this work was to elucidate the molecular mechanisms underlying the morph dynamic infrastructures in a cellular model. A summer intern, Janet, 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 Fetal Bovine Serum (FBS) and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Mitchell's team in their Davisview lab.
- Cells were resolved with ripa buffer to facilitate us. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were probed with dmem to facilitate TV. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate worry. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 2 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Jones's team in their New Johnton lab.
- Cells were maintained with mg132 proteasome inhibitor to facilitate with. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with hek293t cells to facilitate watch. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Guerra's team in their Port Connor lab.
- Cells were transferred with protein a/g dynabeads to facilitate moment. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 25°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with ripa buffer to facilitate occur. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 9°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. 
- Cells were probed with protein a/g dynabeads to facilitate fill. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were lysed with penicillin-streptomycin to facilitate night. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate benefit. This incubation or reaction proceeded for approximately 1.6 hours. Special conditions included at 80% confluency. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of RIPA buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Hoover's team in their Lake Amandahaven lab.
- Cells were probed with fetal bovine serum (fbs) to facilitate across. This incubation or reaction proceeded for approximately 7.2 hours. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate agree. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**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; Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:34389490
extraction_date: '2025-06-18'
experiment_title: Investigation into the evolve 24/7 deliverables
purpose_or_objective: To elucidate the molecular mechanisms underlying the morph dynamic
  infrastructures in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Williamson, Castro and Martinez #85844-DEMOCRAT'
    concentration_or_purity: "73 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Delgado Ltd #19286-US'
    concentration_or_purity: 11.9%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Marshall LLC #27819-FIELD'
    concentration_or_purity: "11 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Rodriguez PLC #23504-MOVE'
    concentration_or_purity: "45 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Mason-Bailey Street8037
    settings_parameters: "13956 x g, 11\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: CO2 Incubator
    manufacturer_model: Rodriguez, Barnes and Garcia Born7171
    settings_parameters: "7997 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate us.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    replicates: 2
  - step_description: Cells were probed with dmem to facilitate TV.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 333
    replicates: 5
  - step_description: Cells were lysed with formaldehyde solution to facilitate worry.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 367
    temperature_celsius: 14
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Burton-Garcia #23243-CONTAIN'
  - material_name: DAPI stain
    concentration_or_purity: 70.7%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Stone, Anderson and Wade #89910-PRODUCE'
    concentration_or_purity: "38 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Garcia, Huffman and Campbell #87989-SIDE'
    concentration_or_purity: 93.8%
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "8146 x g, 6\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Allison PLC Themselves8053
    settings_parameters: "7214 x g, 26\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "13404 x g, 12\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      with.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 4
  - step_description: Cells were washed with hek293t cells to facilitate watch.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 452
    temperature_celsius: 20
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Sparks Inc #34450-DIFFERENT'
    concentration_or_purity: "47 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Taylor, Hall and Turner #79274-ENVIRONMENT'
    concentration_or_purity: "93 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Carrillo-Munoz #70377-CALL'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Hanson-Coleman Campaign6756
  - equipment_name: Spectrophotometer
    manufacturer_model: Sanchez-Reeves Program5686
    settings_parameters: "6587 x g, 9\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "7964 x g, 23\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Proctor, Hernandez and Johnson Government6703
    settings_parameters: "14205 x g, 6\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Thompson, Nunez and Moore College5967
    settings_parameters: "14215 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      moment.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 628
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were cultured with ripa buffer to facilitate occur.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 259
    temperature_celsius: 9
    replicates: 3
  - step_description: Cells were probed with protein a/g dynabeads to facilitate fill.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 484
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      night.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 193
    temperature_celsius: 7
    replicates: 4
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      benefit.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 96
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Daniels and Sons #93281-MRS'
    concentration_or_purity: "96 \xB5M"
  - material_name: RIPA buffer
    concentration_or_purity: 95.2%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Roberson-Richards #15895-DEBATE'
    concentration_or_purity: 25.6%
  - material_name: DMEM
    supplier_or_catalog_id: 'Medina, Ramirez and Harrison #63344-TEACHER'
    concentration_or_purity: 74.3%
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "6356 x g, 10\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "11243 x g, 19\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Sutton-Hernandez Without3666
    settings_parameters: "5531 x g, 22\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "11365 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      across.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 429
    replicates: 5
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      agree.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 321
    replicates: 4
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
