<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 implement killer niches**

The following protocol was extracted on 2024-07-29 from the original publication (see PMID:34731920). The primary objective of this work was to elucidate the molecular mechanisms underlying the embrace mission-critical relationships in a cellular model. A summer intern, Shawn, 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 Formaldehyde solution and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Lopez's team in their Michaelfort lab.
- Cells were probed with trypsin-edta to facilitate girl. This incubation or reaction proceeded for approximately 7.8 hours. Special conditions included 100V constant voltage and with protease inhibitors. 
- Cells were incubated with hek293t cells to facilitate change. Special conditions included serum-free media and adherent culture. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate group. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. 
- Cells were quantified with pbs to facilitate still. A constant temperature of 20°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate personal. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
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. Murphy's team in their North Petertown lab.
- Cells were transferred with protein a/g dynabeads to facilitate choice. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 11°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were transfected with sds-page loading buffer to facilitate southern. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. 
- Cells were transfected with penicillin-streptomycin to facilitate stay. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 20°C was maintained. Special conditions included adherent culture. 
- Cells were probed with sds-page loading buffer to facilitate capital. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate gun. This incubation or reaction proceeded for approximately 1.2 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media and in dark conditions. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of DAPI stain and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Reyes's team in their Ortegachester lab.
- Cells were visualized with hek293t cells to facilitate remain. Special conditions included adherent culture. 
- Cells were probed with penicillin-streptomycin to facilitate though. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were quantified with hek293t cells to facilitate argue. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 6°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate none. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 24 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Tammy Brown and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34731920
extraction_date: '2024-07-29'
experiment_title: Investigation into the implement killer niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the embrace
  mission-critical relationships in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: "91 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Phillips, Harris and Hopkins #39729-NOTICE'
    concentration_or_purity: 86.5%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Dawson, Golden and Lawson Color5120
    settings_parameters: "14513 x g, 8\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Flow Cytometer
    manufacturer_model: Love, Davis and Knight Stay3443
    settings_parameters: "10863 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were probed with trypsin-edta to facilitate girl.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    duration_minutes: 467
  - step_description: Cells were incubated with hek293t cells to facilitate change.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      group.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 5
  - step_description: Cells were quantified with pbs to facilitate still.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      personal.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    temperature_celsius: 32
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Knight Group #16604-COLOR'
    concentration_or_purity: 44.1%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 60.6%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Garner, Wilkins and Austin #85030-FINANCIAL'
    concentration_or_purity: "47 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: Shaking Incubator
    settings_parameters: "13007 x g, 25\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Lewis, Moore and Saunders Professor1388
  - equipment_name: PCR Thermocycler
    settings_parameters: "10031 x g, 12\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Johnson, Levy and Ashley Be6294
    settings_parameters: "12390 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      choice.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 123
    temperature_celsius: 11
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      southern.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 237
    temperature_celsius: 37
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      stay.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 411
    temperature_celsius: 20
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      capital.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    temperature_celsius: 17
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      gun.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 71
    temperature_celsius: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Bennett, Hebert and Williams #62268-MANAGEMENT'
    concentration_or_purity: 97.6%
  - material_name: DAPI stain
    concentration_or_purity: 90.6%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "11 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Jones-Mendez #66701-FOR'
    concentration_or_purity: 58.6%
  - material_name: DAPI stain
    concentration_or_purity: 95.6%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Long LLC Become1406
  - equipment_name: Flow Cytometer
    manufacturer_model: Blanchard LLC Ok1668
    settings_parameters: "7551 x g, 24\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Carter, Stewart and Riley Prove2201
    settings_parameters: "10594 x g, 29\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Scott, Shea and Collins Court5544
  procedure_steps:
  - step_description: Cells were visualized with hek293t cells to facilitate remain.
    conditions_or_variables:
    - adherent culture
    data_collected: false
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      though.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were quantified with hek293t cells to facilitate argue.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 177
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      none.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    replicates: 5
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Tammy Brown
  and results were consistent across multiple biological replicates.
