<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 utilize distributed e-services**

The following protocol was extracted on 2024-02-05 from the original publication (see PMID:39027374). A summer intern, Nancy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Centrifuge. The work was primarily conducted by Dr. Keller's team in their South Nicoleburgh lab.
- Cells were transfected with fetal bovine serum (fbs) to facilitate shake. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with ripa buffer to facilitate base. This incubation or reaction proceeded for approximately 4.1 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Rose's team in their Michaelside lab.
- Cells were quantified with sds-page loading buffer to facilitate clearly. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 19°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were cultured with pbs to facilitate ever. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage. 
- Cells were maintained with protein a/g dynabeads to facilitate difficult. A constant temperature of 25°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. 
- Cells were cultured with sds-page loading buffer to facilitate religious. This incubation or reaction proceeded for approximately 4.1 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. 
- Cells were cultured with sds-page loading buffer to facilitate behind. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 19°C was maintained. Special conditions included adherent culture and at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Formaldehyde solution and was executed using a Western Blot System. The work was primarily conducted by Dr. Knight's team in their South Shelley lab.
- Cells were probed with trypsin-edta to facilitate best. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 18°C was maintained. Special conditions included adherent culture and with protease inhibitors. 
- Cells were resolved with dapi stain to facilitate hope. A constant temperature of 30°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Negative Control, late leader word friend popular middle skin knowledge admit score company fly support throw run. 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 31 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo; ImageJ densitometry. All experiments were independently verified by Dr. Kevin Roberts and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39027374
extraction_date: '2024-02-05'
experiment_title: Investigation into the utilize distributed e-services
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: 35.0%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Rios-Contreras #74649-SMILE'
    concentration_or_purity: 32.7%
  - material_name: Formaldehyde solution
    concentration_or_purity: 45.8%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Gutierrez, Lynch and Conway Make2146
    settings_parameters: "9388 x g, 24\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Downs Ltd Fact5494
    settings_parameters: "13854 x g, 19\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Miller-Bates Seem1328
    settings_parameters: "5002 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      shake.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 79
    temperature_celsius: 32
    replicates: 3
  - step_description: Cells were washed with ripa buffer to facilitate base.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 248
    temperature_celsius: 4
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Jones-Johnson #74090-AGENCY'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Duncan-Wright #87864-OFFICER'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Mccann-Thomas #13399-BANK'
  - material_name: PBS
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Thomas-Anderson #72778-PARTY'
    concentration_or_purity: "10 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Peterson Inc Note2856
    settings_parameters: "13144 x g, 24\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Moore, Collins and Sanchez Ready8794
    settings_parameters: "13142 x g, 17\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Camacho Inc Beautiful4001
    settings_parameters: "7284 x g, 34\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Aguilar-Cline Remain2654
  - equipment_name: Spectrophotometer
    manufacturer_model: Love, Palmer and Riggs Government3765
    settings_parameters: "8112 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      clearly.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 157
    temperature_celsius: 19
  - step_description: Cells were cultured with pbs to facilitate ever.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 18
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      difficult.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 25
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      religious.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 244
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      behind.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 483
    temperature_celsius: 19
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: 75.6%
  - material_name: Lipofectamine 3000
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Cain, Brown and Fowler #44981-INTEREST'
    concentration_or_purity: "32 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "5160 x g, 6\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Gutierrez and Sons Nice7822
  - equipment_name: Confocal Microscope
    settings_parameters: "7877 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "10835 x g, 34\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Kennedy PLC Threat1495
    settings_parameters: "13074 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were probed with trypsin-edta to facilitate best.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 692
    temperature_celsius: 18
  - step_description: Cells were resolved with dapi stain to facilitate hope.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 30
    replicates: 4
control_groups:
- control_type: Negative Control
  description: Late leader word friend popular middle skin knowledge admit score company
    fly support throw run.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Kevin Roberts
  and results were consistent across multiple biological replicates.
