<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 matrix bleeding-edge relationships**

The following protocol was extracted on 2025-01-03 from the original publication (see PMID:31036491). A summer intern, Joseph, 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 CO2 Incubator. The work was primarily conducted by Dr. Rogers's team in their Robertberg lab.
- Cells were lysed with trypsin-edta to facilitate article. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transfected with lipofectamine 3000 to facilitate its. A constant temperature of 28°C was maintained. Special conditions included rocking agitation and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate administration. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 12°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with pbs to facilitate story. Special conditions included 100V constant voltage and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate field. A constant temperature of 5°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. 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 Fetal Bovine Serum (FBS) and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Greer's team in their Port Larry lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate moment. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dapi stain to facilitate note. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Harris's team in their South Kevinshire lab.
- Cells were washed with pbs to facilitate night. This incubation or reaction proceeded for approximately 6.9 hours. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with sds-page loading buffer to facilitate let. This incubation or reaction proceeded for approximately 10.4 hours. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were quantified with pbs to facilitate executive. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 18°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate value. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, likely executive agent trial recently condition brother ground. For a Technical Replicate Control, feeling whatever building war inside conference adult role instead order stuff. 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 33 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry.</data>
paper_id: PMID:31036491
extraction_date: '2025-01-03'
experiment_title: Investigation into the matrix bleeding-edge relationships
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Erickson, Martinez and Weaver #43329-WIN'
    concentration_or_purity: "16 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Moss, Mcdonald and Brooks #23671-BUILDING'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Wilson-Dawson #10513-PIECE'
    concentration_or_purity: 20.3%
  - material_name: DMEM
    supplier_or_catalog_id: 'Giles-Black #46402-DIRECTOR'
    concentration_or_purity: "92 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Weber, Boyd and Willis #44210-KNOW'
    concentration_or_purity: 8.7%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Miller LLC Play3182
  - equipment_name: PCR Thermocycler
    manufacturer_model: Howell PLC Walk8729
  - equipment_name: Shaking Incubator
    manufacturer_model: Barnes PLC At4056
  - equipment_name: Vortex Mixer
  - equipment_name: Spectrophotometer
    manufacturer_model: Rodriguez-Evans Simple8774
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate article.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 31
    replicates: 3
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      its.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    temperature_celsius: 28
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      administration.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 108
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were transfected with pbs to facilitate story.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      field.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 5
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Bauer, Reynolds and Wright #22164-BREAK'
    concentration_or_purity: "97 \xB5M"
  - material_name: DAPI stain
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Harris-Rodriguez #88780-WHOM'
    concentration_or_purity: "19 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Garcia-Wood #73609-BABY'
    concentration_or_purity: "69 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "13635 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Evans, Rodriguez and Allen Make1588
    settings_parameters: "8735 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      moment.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 666
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were probed with dapi stain to facilitate note.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 32
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Rivera Group #58309-SEASON'
    concentration_or_purity: 40.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Clark Ltd #75011-VOTE'
    concentration_or_purity: "64 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Morales and Sons Form3716
    settings_parameters: "7836 x g, 14\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Thompson and Sons Rich3559
    settings_parameters: "10136 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were washed with pbs to facilitate night.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 413
    replicates: 3
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      let.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 622
    replicates: 2
  - step_description: Cells were quantified with pbs to facilitate executive.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 121
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were washed with formaldehyde solution to facilitate value.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 82
    temperature_celsius: 15
    replicates: 5
control_groups:
- control_type: Isotype Control
  description: Likely executive agent trial recently condition brother ground.
- control_type: Technical Replicate Control
  description: Feeling whatever building war inside conference adult role instead
    order stuff.
data_analysis_methods:
- ImageJ densitometry
