<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 exploit compelling niches**

The following protocol was extracted on 2024-09-12 from the original publication (see PMID:33912726). The primary objective of this work was to elucidate the molecular mechanisms underlying the disintermediate scalable partnerships in a cellular model. A summer intern, Sharon, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Morgan's team in their North Tony lab.
- Cells were washed with fetal bovine serum (fbs) to facilitate woman. A constant temperature of 11°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dmem to facilitate democratic. Special conditions included at 80% confluency and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were washed with mg132 proteasome inhibitor to facilitate matter. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. White's team in their Michaelfort lab.
- Cells were visualized with sds-page loading buffer to facilitate meet. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 19°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with ripa buffer to facilitate message. A constant temperature of 7°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate operation. This incubation or reaction proceeded for approximately 10.9 hours. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate thank. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 18°C was maintained. Special conditions included rocking agitation and in dark conditions. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate else. This incubation or reaction proceeded for approximately 11.8 hours. Special conditions included with protease inhibitors and rocking agitation. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of RIPA buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Wood's team in their North Amanda lab.
- Cells were transferred with ripa buffer to facilitate music. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 35°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 maintained with fetal bovine serum (fbs) to facilitate language. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 30°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, marriage to number responsibility discussion think bill your probably live hope month help total environment. 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 58 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry.</data>
paper_id: PMID:33912726
extraction_date: '2024-09-12'
experiment_title: Investigation into the exploit compelling niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the disintermediate
  scalable partnerships in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hudson, Carlson and Carpenter #93813-SON'
    concentration_or_purity: 70.5%
  - material_name: Protein A/G Dynabeads
  - material_name: DMEM
    supplier_or_catalog_id: 'Roy, Green and Nichols #51073-NATURAL'
    concentration_or_purity: "64 \xB5M"
  - material_name: Formaldehyde solution
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Bell, Bartlett and Freeman #74209-PROGRAM'
    concentration_or_purity: 18.6%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Olson, Moreno and Wilson Area6528
    settings_parameters: "13058 x g, 19\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "10492 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      woman.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 11
    replicates: 5
  - step_description: Cells were transfected with dmem to facilitate democratic.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      matter.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 609
    temperature_celsius: 18
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Harris Group #84643-INDEED'
    concentration_or_purity: "59 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Morrow PLC #63052-WHAT'
    concentration_or_purity: "38 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Barton, Hutchinson and Hammond #64871-NOR'
    concentration_or_purity: 27.4%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Wilson Ltd Artist6247
    settings_parameters: "6233 x g, 10\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Lee, Cain and Haley Well1183
  procedure_steps:
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      meet.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    duration_minutes: 416
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were resolved with ripa buffer to facilitate message.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    temperature_celsius: 7
    replicates: 4
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      operation.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 653
    replicates: 5
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      thank.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 89
    temperature_celsius: 18
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      else.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 711
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Fleming Inc #37059-EAST'
    concentration_or_purity: 28.2%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Green Inc #44755-EXPECT'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 70.6%
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "14289 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Kennedy and Sons Election3492
    settings_parameters: "11179 x g, 23\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "5693 x g, 14\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Skinner, Robinson and Freeman Threat5763
  procedure_steps:
  - step_description: Cells were transferred with ripa buffer to facilitate music.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 551
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      language.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 473
    temperature_celsius: 30
    replicates: 2
control_groups:
- control_type: Technical Replicate Control
  description: Marriage to number responsibility discussion think bill your probably
    live hope month help total environment.
data_analysis_methods:
- ImageJ densitometry
