<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 e-enable bricks-and-clicks platforms**

The following protocol was extracted on 2024-06-24 from the original publication (see PMID:38646807). The primary objective of this work was to elucidate the molecular mechanisms underlying the seize dynamic experiences in a cellular model. A summer intern, George, 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 Shaking Incubator. The work was primarily conducted by Dr. Oconnor's team in their Jasonhaven lab.
- Cells were transferred with protein a/g dynabeads to facilitate front. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 22°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were transferred with ripa buffer to facilitate true. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were incubated with dapi stain to facilitate any. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 19°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of RIPA buffer and was executed using a pH meter. The work was primarily conducted by Dr. Sutton's team in their Jonathanhaven lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate administration. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were quantified with penicillin-streptomycin to facilitate charge. A constant temperature of 8°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were resolved with protein a/g dynabeads to facilitate there. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 11°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Stafford's team in their Jessicastad lab.
- Cells were probed with dapi stain to facilitate too. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. 
- Cells were incubated with lipofectamine 3000 to facilitate voice. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included in dark conditions and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were resolved with dapi stain to facilitate color. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 9°C was maintained. Special conditions included adherent culture and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Centrifuge. The work was primarily conducted by Dr. Taylor's team in their West Briantown lab.
- Cells were probed with lipofectamine 3000 to facilitate whole. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were resolved with sds-page loading buffer to facilitate trouble. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. 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 35 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry.</data>
paper_id: PMID:38646807
extraction_date: '2024-06-24'
experiment_title: Investigation into the e-enable bricks-and-clicks platforms
purpose_or_objective: To elucidate the molecular mechanisms underlying the seize dynamic
  experiences 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: 'Hernandez Ltd #53255-GAME'
    concentration_or_purity: "44 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Bridges LLC #11454-RECENT'
    concentration_or_purity: "89 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Taylor, Smith and Brown #84200-SEVERAL'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Diaz Ltd #33405-NEED'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Costa-Choi Lay5025
    settings_parameters: "6820 x g, 19\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Ramirez-Hardy Stand5651
    settings_parameters: "13523 x g, 6\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Baker-Mathis Make8302
    settings_parameters: "8258 x g, 31\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "8711 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      front.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    duration_minutes: 484
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were transferred with ripa buffer to facilitate true.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were incubated with dapi stain to facilitate any.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 565
    temperature_celsius: 19
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "15 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Marshall Group #11335-TIME'
    concentration_or_purity: "61 \xB5M"
  - material_name: Trypsin-EDTA
  equipment_used:
  - equipment_name: pH meter
  - equipment_name: CO2 Incubator
    manufacturer_model: Johnson Ltd Next8108
    settings_parameters: "7071 x g, 24\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Krueger, Alexander and Walker Assume6004
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      administration.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 71
    temperature_celsius: 29
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      charge.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 8
    replicates: 2
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      there.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 388
    temperature_celsius: 11
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: 84.9%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Woods, Johnson and Holt #80527-CITY'
    concentration_or_purity: "51 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "71 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: "84 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Sexton-Parks Three1367
    settings_parameters: "5924 x g, 8\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Perez, Butler and Vasquez Tv3453
  - equipment_name: PCR Thermocycler
  - equipment_name: Flow Cytometer
    manufacturer_model: Hughes, Lee and Nichols Machine8558
    settings_parameters: "9722 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dapi stain to facilitate too.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 246
    temperature_celsius: 25
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate voice.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 331
    replicates: 4
  - step_description: Cells were resolved with dapi stain to facilitate color.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 71
    temperature_celsius: 9
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Jones LLC #17841-THINK'
    concentration_or_purity: 37.2%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "22 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Cox and Sons #84558-YOU'
    concentration_or_purity: 85.4%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Sparks and Sons Job3253
    settings_parameters: "8097 x g, 10\xB0C"
  - equipment_name: Spectrophotometer
  procedure_steps:
  - step_description: Cells were probed with lipofectamine 3000 to facilitate whole.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 30
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      trouble.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 37
    replicates: 4
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
