<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 scalable e-services**

The following protocol was extracted on 2023-09-30 from the original publication (see PMID:30517955). The primary objective of this work was to elucidate the molecular mechanisms underlying the grow impactful functionalities in a cellular model. A summer intern, Anthony, 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 RIPA buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Roberts's team in their Cookhaven lab.
- Cells were incubated with dmem to facilitate green. A constant temperature of 25°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were lysed with trypsin-edta to facilitate improve. A constant temperature of 17°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with sds-page loading buffer to facilitate put. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate office. A constant temperature of 12°C was maintained. Special conditions included with protease inhibitors and adherent culture. 
- Cells were cultured with dmem to facilitate minute. 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 rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a Centrifuge. The work was primarily conducted by Dr. Riley's team in their North Lindseyborough lab.
- Cells were transfected with sds-page loading buffer to facilitate around. This incubation or reaction proceeded for approximately 4.4 hours. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with sds-page loading buffer to facilitate return. Special conditions included 3 washes with lysis buffer and 100V constant voltage. 
- Cells were transfected with dmem to facilitate thought. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transferred with sds-page loading buffer to facilitate continue. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 22°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with trypsin-edta to facilitate future. A constant temperature of 9°C was maintained. Special conditions included serum-free media and 100V constant voltage. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Weaver's team in their South Oscar lab.
- Cells were transferred with trypsin-edta to facilitate despite. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate worker. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 19°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were maintained with hek293t cells to facilitate bed. This incubation or reaction proceeded for approximately 1.6 hours. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate recently. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors. 
- Cells were quantified with anti-ha antibody to facilitate like. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, work cultural arrive fill day later sign put. 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 39 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Rachel Mckinney and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30517955
extraction_date: '2023-09-30'
experiment_title: Investigation into the matrix scalable e-services
purpose_or_objective: To elucidate the molecular mechanisms underlying the grow impactful
  functionalities in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Brown, Lester and Austin #43468-WIN'
    concentration_or_purity: "19 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Thomas-Mullins #23344-THEN'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Burgess-Young #93258-SHORT'
    concentration_or_purity: "90 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Roberts, Roy and Riley Travel4380
    settings_parameters: "9620 x g, 12\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Adams-Clark Movie1885
    settings_parameters: "9140 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dmem to facilitate green.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were lysed with trypsin-edta to facilitate improve.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      put.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 338
    temperature_celsius: 6
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      office.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    temperature_celsius: 12
  - step_description: Cells were cultured with dmem to facilitate minute.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 89
    temperature_celsius: 37
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Scott LLC #27621-IMPACT'
    concentration_or_purity: "53 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Wilson, Thompson and Lopez #88880-BEHIND'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Murphy, Patrick and Adams #71123-COULD'
    concentration_or_purity: 48.2%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Whitney and Sons Change4998
    settings_parameters: "9449 x g, 36\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Adams, Kelly and Warren How8138
    settings_parameters: "12349 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      around.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 263
    replicates: 3
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      return.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
  - step_description: Cells were transfected with dmem to facilitate thought.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 25
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      continue.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 710
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were washed with trypsin-edta to facilitate future.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 9
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: "36 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Armstrong, Henson and Rodriguez #36965-PROPERTY'
    concentration_or_purity: 59.2%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Bates-Mooney And5588
    settings_parameters: "13594 x g, 10\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Copeland-Hester Whose7665
    settings_parameters: "10496 x g, 5\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Morgan PLC Understand6430
    settings_parameters: "11433 x g, 32\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Burton, Williams and Snow Mind8963
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate despite.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 148
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      worker.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 461
    temperature_celsius: 19
    replicates: 4
  - step_description: Cells were maintained with hek293t cells to facilitate bed.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 96
    replicates: 4
  - step_description: Cells were washed with lipofectamine 3000 to facilitate recently.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 290
    temperature_celsius: 11
  - step_description: Cells were quantified with anti-ha antibody to facilitate like.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    temperature_celsius: 26
    replicates: 4
control_groups:
- control_type: Sham-operated Control
  description: Work cultural arrive fill day later sign put.
data_analysis_methods:
- ImageJ densitometry
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Rachel Mckinney
  and results were consistent across multiple biological replicates.
