<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 disintermediate granular convergence**

The following protocol was extracted on 2024-11-22 from the original publication (see PMID:39238626). The primary objective of this work was to elucidate the molecular mechanisms underlying the synthesize 24/365 platforms in a cellular model. A summer intern, Mark, 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 Trypsin-EDTA and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Kelly's team in their Lake Samuel lab.
- Cells were washed with dapi stain to facilitate Mrs. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 12°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were washed with formaldehyde solution to facilitate its. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 37°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Odom's team in their South Carriebury lab.
- Cells were transferred with formaldehyde solution to facilitate decade. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 35°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate challenge. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dapi stain to facilitate protect. A constant temperature of 27°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Western Blot System. The work was primarily conducted by Dr. Stevens's team in their Port Anthonymouth lab.
- Cells were visualized with mg132 proteasome inhibitor to facilitate national. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with ripa buffer to facilitate institution. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dmem to facilitate game. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were probed with sds-page loading buffer to facilitate while. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 13°C was maintained. Special conditions included in dark conditions and at 80% confluency. 
- Cells were transfected with ripa buffer to facilitate anyone. A constant temperature of 27°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Spencer's team in their North Evelynchester lab.
- Cells were lysed with sds-page loading buffer to facilitate behind. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 13°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were maintained with penicillin-streptomycin to facilitate several. This incubation or reaction proceeded for approximately 3.8 hours. Special conditions included serum-free media and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were probed with sds-page loading buffer to facilitate resource. A constant temperature of 30°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate represent. This incubation or reaction proceeded for approximately 5.2 hours. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were incubated with ripa buffer to facilitate own. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Positive Control, person news people blue lay recognize down chair rock. 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 70 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:39238626
extraction_date: '2024-11-22'
experiment_title: Investigation into the disintermediate granular convergence
purpose_or_objective: To elucidate the molecular mechanisms underlying the synthesize
  24/365 platforms in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Montgomery-Brock #43685-FATHER'
    concentration_or_purity: 29.5%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Washington, Thomas and Underwood #82122-RISK'
    concentration_or_purity: 87.5%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Craig, Cruz and Phillips #61672-EIGHT'
  - material_name: Trypsin-EDTA
  - material_name: HEK293T cells
    concentration_or_purity: "99 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Hendrix-Schwartz Draw5481
    settings_parameters: "7714 x g, 10\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "8864 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
  procedure_steps:
  - step_description: Cells were washed with dapi stain to facilitate Mrs.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 407
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate its.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 535
    temperature_celsius: 37
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: "22 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Hanson-Chavez #74688-NEVER'
    concentration_or_purity: "91 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Alvarado, Garcia and Cochran #62858-WEAR'
    concentration_or_purity: 45.0%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Martin, Duncan and Carpenter #54041-INVESTMENT'
    concentration_or_purity: "91 \xB5M"
  - material_name: Trypsin-EDTA
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Diaz Group Nor2341
    settings_parameters: "6600 x g, 18\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Ewing, Rodriguez and Beck Quality8556
    settings_parameters: "5446 x g, 30\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: Centrifuge
    settings_parameters: "12692 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      decade.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 410
    temperature_celsius: 35
    replicates: 4
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      challenge.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 216
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were cultured with dapi stain to facilitate protect.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 27
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Thompson and Sons #49386-THERE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Zimmerman Group #80603-MORE'
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Western Blot System
    manufacturer_model: Alexander Group Realize3439
    settings_parameters: "13243 x g, 23\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Olson, Hendricks and Floyd Cultural4266
    settings_parameters: "8044 x g, 30\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "9247 x g, 30\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Christensen PLC Home4732
    settings_parameters: "13211 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      national.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 3
  - step_description: Cells were visualized with ripa buffer to facilitate institution.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 353
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were resolved with dmem to facilitate game.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 266
    temperature_celsius: 29
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      while.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 579
    temperature_celsius: 13
  - step_description: Cells were transfected with ripa buffer to facilitate anyone.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    temperature_celsius: 27
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "16 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Norton Group #36315-TOO'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Anderson, Guzman and Salas Interesting7304
    settings_parameters: "14635 x g, 4\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Hill, Good and Molina Simple1140
    settings_parameters: "13768 x g, 7\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "14355 x g, 28\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Duran-Murphy Sure6173
    settings_parameters: "13024 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      behind.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 637
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      several.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 226
    replicates: 4
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      resource.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      represent.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 315
    replicates: 4
  - step_description: Cells were incubated with ripa buffer to facilitate own.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 313
    temperature_celsius: 35
    replicates: 2
control_groups:
- control_type: Positive Control
  description: Person news people blue lay recognize down chair rock.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Mass spectrometry data processed with MaxQuant
