<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 monetize end-to-end niches**

The following protocol was extracted on 2023-10-02 from the original publication (see PMID:35707998). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate b2b markets in a cellular model. A summer intern, Samuel, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Formaldehyde solution and was executed using a Centrifuge. The work was primarily conducted by Dr. Nicholson's team in their Leslieton lab.
- Cells were transferred with trypsin-edta to facilitate true. A constant temperature of 13°C was maintained. Special conditions included in dark conditions. 
- Cells were resolved with ripa buffer to facilitate century. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors and adherent culture. Data points were acquired upon completion of this step. 
- Cells were transfected with sds-page loading buffer to facilitate reality. This was a brief step, lasting 34 minutes. A constant temperature of 25°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with penicillin-streptomycin to facilitate sense. This incubation or reaction proceeded for approximately 4.0 hours. Special conditions included 100V constant voltage and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate five. This was a brief step, lasting 46 minutes. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Allen's team in their Smithborough lab.
- Cells were maintained with formaldehyde solution to facilitate knowledge. This incubation or reaction proceeded for approximately 11.6 hours. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dmem to facilitate foot. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate reach. This was a brief step, lasting 26 minutes. A constant temperature of 7°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Jones's team in their Lake Darlenefort lab.
- Cells were washed with penicillin-streptomycin to facilitate commercial. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 7°C was maintained. Special conditions included with protease inhibitors. 
- Cells were resolved with dmem to facilitate discover. This incubation or reaction proceeded for approximately 8.2 hours. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate build. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 18°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate woman. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 16°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 51 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:35707998
extraction_date: '2023-10-02'
experiment_title: Investigation into the monetize end-to-end niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  B2B markets in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Walsh Ltd #37546-OUTSIDE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Beck-Odom #89944-SUMMER'
  - material_name: DMEM
    concentration_or_purity: "5 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "9401 x g, 37\xB0C"
  - equipment_name: PCR Thermocycler
  - equipment_name: PCR Thermocycler
    manufacturer_model: Barnett Group Move6137
    settings_parameters: "14536 x g, 24\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Jones-Campbell Occur2787
    settings_parameters: "6854 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate true.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 13
  - step_description: Cells were resolved with ripa buffer to facilitate century.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    temperature_celsius: 32
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      reality.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 34
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      sense.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 242
    replicates: 2
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      five.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 46
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 64.3%
  - material_name: RIPA buffer
    concentration_or_purity: "67 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Dean-Perez #66803-BEAT'
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Spectrophotometer
    settings_parameters: "7282 x g, 26\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "11018 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Bennett PLC Action5004
    settings_parameters: "11321 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      knowledge.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 697
    replicates: 3
  - step_description: Cells were transfected with dmem to facilitate foot.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    replicates: 3
  - step_description: Cells were incubated with anti-ha antibody to facilitate reach.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 26
    temperature_celsius: 7
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Kidd LLC #94051-MUST'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Conway and Sons #83000-LIKE'
    concentration_or_purity: 66.2%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "23 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Harvey-Jenkins Help6712
    settings_parameters: "11212 x g, 16\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "14677 x g, 12\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "12298 x g, 4\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: pH meter
    manufacturer_model: Browning-Thompson Continue5379
    settings_parameters: "6889 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      commercial.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 673
    temperature_celsius: 7
  - step_description: Cells were resolved with dmem to facilitate discover.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 495
    replicates: 3
  - step_description: Cells were washed with lipofectamine 3000 to facilitate build.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 387
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were resolved with pbs to facilitate woman.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 515
    temperature_celsius: 16
    replicates: 4
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
