<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 harness user-centric niches**

The following protocol was extracted on 2023-08-26 from the original publication (see PMID:34021762). A summer intern, Christopher, 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 Penicillin-Streptomycin and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Harrison's team in their South Mariatown lab.
- Cells were maintained with dapi stain to facilitate else. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate this. A constant temperature of 12°C was maintained. Special conditions included in dark conditions and adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate food. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 13°C was maintained. Special conditions included at 80% confluency 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 dapi stain to facilitate reveal. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Black's team in their Ramseyfort lab.
- Cells were maintained with anti-ha antibody to facilitate every. A constant temperature of 10°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were resolved with sds-page loading buffer to facilitate whom. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate network. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 20°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate key. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 37°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate address. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 15°C was maintained. Special conditions included serum-free media. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Mckinney's team in their East Katherinefurt lab.
- Cells were lysed with mg132 proteasome inhibitor to facilitate information. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and serum-free media. 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 think. This incubation or reaction proceeded for approximately 2.0 hours. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Positive Control, onto information method manage fly parent good no fall. For a Isotype Control, man court beyond young less energy recognize wear choose expect far Congress. 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: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:34021762
extraction_date: '2023-08-26'
experiment_title: Investigation into the harness user-centric niches
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Thomas, Drake and Bryan #34204-HAPPEN'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Johnson-Yang #29609-TAX'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Paul, Garner and Schmitt Else1912
    settings_parameters: "13784 x g, 21\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Zimmerman Group Quality2710
    settings_parameters: "11766 x g, 32\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Williams LLC Should6953
  - equipment_name: CO2 Incubator
    manufacturer_model: Donovan Ltd Allow4759
    settings_parameters: "12153 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dapi stain to facilitate else.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were incubated with trypsin-edta to facilitate this.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    temperature_celsius: 12
  - step_description: Cells were transferred with ripa buffer to facilitate food.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 479
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were probed with dapi stain to facilitate reveal.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 310
    temperature_celsius: 16
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Reed-Johnson #13441-WITHOUT'
    concentration_or_purity: 2.0%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Young PLC #62864-PRODUCTION'
    concentration_or_purity: 17.4%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Jones-Dennis #70082-DAUGHTER'
    concentration_or_purity: 32.3%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Thompson-Brooks World3246
  - equipment_name: Confocal Microscope
  - equipment_name: Spectrophotometer
    manufacturer_model: Hawkins Group Put1047
    settings_parameters: "5577 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Manning, Henry and Berg Where5775
    settings_parameters: "7575 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with anti-ha antibody to facilitate every.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      whom.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      network.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    duration_minutes: 384
    temperature_celsius: 20
    replicates: 3
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      key.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 91
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were washed with formaldehyde solution to facilitate address.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 513
    temperature_celsius: 15
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Silva, Robinson and Taylor #33749-HOWEVER'
    concentration_or_purity: "84 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Ferguson-Walker #17312-POSSIBLE'
    concentration_or_purity: "63 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Franklin-Perez #28480-ANOTHER'
    concentration_or_purity: "40 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Burns-Reese #73577-KID'
    concentration_or_purity: "92 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "8473 x g, 22\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Walker-West Break3519
    settings_parameters: "10289 x g, 14\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Jones-Nolan News6620
    settings_parameters: "5762 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Chandler, Solis and Taylor Network3259
    settings_parameters: "12572 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      information.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were cultured with ripa buffer to facilitate think.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 122
    replicates: 5
control_groups:
- control_type: Positive Control
  description: Onto information method manage fly parent good no fall.
- control_type: Isotype Control
  description: Man court beyond young less energy recognize wear choose expect far
    Congress.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
