Assays

5L bioreactor culture of recombinant strain E. coli CH10-12 in a batch/fed-batch strategy at 37°C (BR02). Protein induction promoted when biomass reached 25 g cdw/L and at 28°C for 12 h

Submitter: Susana Alonso Villela

Assay type: Cultivation Experiment

Technology type: Fed-batch

Investigation: Effect of the induction temperature in nanobody...

Study: Recombinant nanobody CH10-12 production at diff...

Organisms: Escherichia coli

SOPs: No SOPs

Data files: BR02 samples, BioPAT MFCS data for BR02 - part 1, BioPAT MFCS data for BR02 - part 2, Data analysis of the BR02 culture, Gas analysis data for BR02 and BR03

Snapshots: No snapshots

Created: 18th Apr 2025 at 08:16, Last updated: 13th Jun 2025 at 10:35

Fed-batch culture of CH10-12 strain, induction at 29°C - BR06

Scorpion antivenom nanobody production in Escherichia coli (Recombinant bispecific VHH)

5L bioreactor culture of recombinant strain E. coli CH10-12. Protein induction promoter when biomass reached 30 g cdw/L and at 29°C for 38 h

Submitter: Susana Alonso Villela

Assay type: Cultivation Experiment

Technology type: Fed-batch

Investigation: Effect of the induction temperature in nanobody...

Study: Recombinant nanobody CH10-12 and NbF12-10 produ...

Organisms: Escherichia coli

SOPs: No SOPs

Data files: BR06 samples, BioPAT MFCS data for BR06 - part 1, BioPAT MFCS data for BR06 - part 2, Data analysis of the BR06 culture, Gas analysis data for BR06 and BR07

Snapshots: No snapshots

Created: 18th Apr 2025 at 08:50, Last updated: 13th Jun 2025 at 11:13

Fed-batch culture of CH10-12 strain, induction at 30°C - BR03

Scorpion antivenom nanobody production in Escherichia coli (Recombinant bispecific VHH)

5L bioreactor culture of recombinant strain E. coli CH10-12. Protein induction promoter when biomass reached 25 g cdw/L and at 30°C for 10 h

Submitter: Susana Alonso Villela

Assay type: Cultivation Experiment

Technology type: Fed-batch

Investigation: Effect of the induction temperature in nanobody...

Study: Recombinant nanobody CH10-12 production at diff...

Organisms: Escherichia coli

SOPs: No SOPs

Data files: BR03 samples, BioPAT MFCS data for BR03 - part 1, BioPAT MFCS data for BR03 - part 2, Data analysis of the BR03 culture, Gas analysis data for BR02 and BR03

Snapshots: No snapshots

Created: 18th Apr 2025 at 08:30, Last updated: 13th Jun 2025 at 10:49

Fed-batch culture of CH10-12 strain, induction at 32°C - BR07

Scorpion antivenom nanobody production in Escherichia coli (Recombinant bispecific VHH)

5L bioreactor culture of recombinant strain E. coli CH10-12. Protein induction promoter when biomass reached 30 g cdw/L and at 32°C for 35 h

Submitter: Susana Alonso Villela

Assay type: Cultivation Experiment

Technology type: Fed-batch

Investigation: Effect of the induction temperature in nanobody...

Study: Recombinant nanobody CH10-12 and NbF12-10 produ...

Organisms: Escherichia coli

SOPs: No SOPs

Data files: BR07 samples, BioPAT MFCS data for BR07 - part 1, BioPAT MFCS data for BR07 - part 2, Data analysis of the BR07 culture, Gas analysis data for BR06 and BR07

Snapshots: No snapshots

Created: 18th Apr 2025 at 08:51, Last updated: 13th Jun 2025 at 11:20

Fed-batch culture of CH10-12 strain, induction at 33°C - BR04

Scorpion antivenom nanobody production in Escherichia coli (Recombinant bispecific VHH)

5L bioreactor culture of recombinant strain E. coli CH10-12. Protein induction promoter when biomass reached 25 g cdw/L and at 33°C for 6 h

Submitter: Susana Alonso Villela

Assay type: Cultivation Experiment

Technology type: Fed-batch

Investigation: Effect of the induction temperature in nanobody...

Study: Recombinant nanobody CH10-12 production at diff...

Organisms: Escherichia coli

SOPs: No SOPs

Data files: BR04 samples, BioPAT MFCS data for BR04 - part 1, BioPAT MFCS data for BR04 - part 2, Data analysis of the BR04 culture, Gas analysis data for BR04 and BR05

Snapshots: No snapshots

Created: 18th Apr 2025 at 08:30, Last updated: 13th Jun 2025 at 11:03

Fed-batch culture of CH10-12 strain, induction at 37°C - BR05

Scorpion antivenom nanobody production in Escherichia coli (Recombinant bispecific VHH)

5L bioreactor culture of recombinant strain E. coli CH10-12. Protein induction promoter when biomass reached 25 g cdw/L and at 37°C for 6 h

Submitter: Susana Alonso Villela

Assay type: Cultivation Experiment

Technology type: Fed-batch

Investigation: Effect of the induction temperature in nanobody...

Study: Recombinant nanobody CH10-12 production at diff...

Organisms: Escherichia coli

SOPs: No SOPs

Data files: BR05 samples, BioPAT MFCS data for BR05 - part 1, BioPAT MFCS data for BR05 - part 2, Data analysis of the BR05 culture, Gas analysis data for BR04 and BR05

Snapshots: No snapshots

Created: 18th Apr 2025 at 08:31, Last updated: 13th Jun 2025 at 11:07

Fed-batch culture of NbF12-10 strain, induction at 29°C - BR08

Scorpion antivenom nanobody production in Escherichia coli (Recombinant bispecific VHH)

5L bioreactor culture of recombinant strain E. coli NbF12-10. Protein induction promoter when biomass reached 30 g cdw/L and at 29°C for 37 h

Submitter: Susana Alonso Villela

Assay type: Cultivation Experiment

Technology type: Fed-batch

Investigation: Effect of the induction temperature in nanobody...

Study: Recombinant nanobody CH10-12 and NbF12-10 produ...

Organisms: Escherichia coli

SOPs: No SOPs

Data files: BR08 samples, BioPAT MFCS data for BR08 - part 1, BioPAT MFCS data for BR08 - part 2, Data analysis of the BR08 culture, Gas analysis data for BR08 and BR09

Snapshots: No snapshots

Created: 18th Apr 2025 at 08:51, Last updated: 13th Jun 2025 at 11:27

Fed-batch culture of WK6 strain, induction at 29°C - BR09

Scorpion antivenom nanobody production in Escherichia coli (Recombinant bispecific VHH)

5L bioreactor culture of reference strain E. coli WK6. Protein induction promoter when biomass reached 25 g cdw/L and at 29°C for 28 h

Submitter: Susana Alonso Villela

Assay type: Cultivation Experiment

Technology type: Fed-batch

Investigation: Effect of the induction temperature in nanobody...

Study: Characterization of E. coli WK6 strain under in...

Organisms: Escherichia coli

SOPs: No SOPs

Data files: BR09 samples, BioPAT MFCS data for BR09 - part 1, BioPAT MFCS data for BR09 - part 2, Data analysis of the BR09 culture, Gas analysis data for BR08 and BR09

Snapshots: No snapshots

Created: 18th Apr 2025 at 08:52, Last updated: 13th Jun 2025 at 11:32

Fed-batch culture of WK6 strain, without induction - BR01

Scorpion antivenom nanobody production in Escherichia coli (Recombinant bispecific VHH)

5L bioreactor culture of strain E. coli WK6 in a batch/fed-batch strategy at 37°C. Characterization of biomass growth and oxygen transfer

Submitter: Susana Alonso Villela

Assay type: Cultivation Experiment

Technology type: Fed-batch

Investigation: Effect of the induction temperature in nanobody...

Study: Characterization of E. coli WK6 strain under ae...

Organisms: Escherichia coli

SOPs: No SOPs

Data files: BR01 samples, BioPAT MFCS data for BR01 - part 1, BioPAT MFCS data for BR01 - part 2, Data analysis of the BR01 culture, Gas analysis data for BR01

Snapshots: No snapshots

Created: 18th Apr 2025 at 07:44, Last updated: 29th Apr 2025 at 14:11

GPI Anchor Predictions

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

No description specified

Submitter: Munazah Andrabi

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: In-silico prediction and mass spectrometric val...

Study: In-Silico Prediction

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 18th May 2020 at 16:05

Growth experiment

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

No description specified

Submitter: Munazah Andrabi

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: In-silico prediction and mass spectrometric val...

Study: Culture experiments

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 18th May 2020 at 16:06

Identify enzymes from spectra

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

No description specified

Submitter: Munazah Andrabi

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: In-silico prediction and mass spectrometric val...

Study: Metabolic model analysis

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 18th May 2020 at 16:35

Liquid chromatography tandem mass spectrometry

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

No description specified

Submitter: Munazah Andrabi

Assay type: Protein Identification

Technology type: Liquid Chromatography-tandom Mass Spectrometry

Investigation: In-silico prediction and mass spectrometric val...

Study: Culture experiments

Organisms: No organisms

SOPs: No SOPs

Data files: Proteins detected by high-throughput mass spect...

Snapshots: No snapshots

Created: 18th May 2020 at 16:31, Last updated: 22nd Jun 2020 at 11:39

Mass Spectrometry Analysis

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

No description specified

Submitter: Munazah Andrabi

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: In-silico prediction and mass spectrometric val...

Study: Validation of the secretome of Aspergillus niger

Organisms: No organisms

SOPs: No SOPs

Data files: Proteins detected by high-throughput mass spect...

Snapshots: No snapshots

Created: 18th May 2020 at 16:32, Last updated: 22nd Jun 2020 at 11:40

Material and water integration

DBTL-P

No description specified

Submitter: Konstantinos Pyrgakis

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Bioprocess design

Study: Bioprocess Integration

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Dec 2020 at 15:43

Modeling of unit processes (reactions, separations recycles)

DBTL-P

No description specified

Submitter: Konstantinos Pyrgakis

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Create/Update model

Study: Bioprocess modeling

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Dec 2020 at 15:43

Obtain metabolic model

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

No description specified

Submitter: Munazah Andrabi

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: In-silico prediction and mass spectrometric val...

Study: Metabolic model analysis

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 18th May 2020 at 16:33

Obtain proteomes

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

No description specified

Submitter: Munazah Andrabi

Assay type: Comparative Genomics

Technology type: Next generation sequencing

Investigation: In-silico prediction and mass spectrometric val...

Study: In-Silico Prediction

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 18th May 2020 at 16:02, Last updated: 18th May 2020 at 16:02

Orthology identification

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

No description specified

Submitter: Munazah Andrabi

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: In-silico prediction and mass spectrometric val...

Study: In-Silico Prediction

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 18th May 2020 at 16:05

Pathway improvement by mutations

DBTL-P

No description specified

Submitter: Konstantinos Pyrgakis

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Computational strain design

Study: Computational strain optimization

Organisms: No organisms

SOPs: Optimal Synthesis of Pathways – II

Data files: No Data files

Snapshots: No snapshots

Created: 16th Dec 2020 at 15:43, Last updated: 10th Feb 2022 at 11:12

Process flowsheeting (process integration and recycles)

DBTL-P

No description specified

Submitter: Konstantinos Pyrgakis

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Create/Update model

Study: Bioprocess modeling

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Dec 2020 at 15:43

Signal Peptide Predictions

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

No description specified

Submitter: Munazah Andrabi

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: In-silico prediction and mass spectrometric val...

Study: In-Silico Prediction

Organisms: No organisms

SOPs: No SOPs

Data files: Aspergillus niger CBS513.88 protein model verif..., Aspergillus niger centered protein clusters wit...

Snapshots: No snapshots

Created: 18th May 2020 at 16:04, Last updated: 3rd Sep 2020 at 13:49

Superstructure modeling and optimization

DBTL-P

No description specified

Submitter: Konstantinos Pyrgakis

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Create/Update model

Study: Bioprocess modeling

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Dec 2020 at 15:43

Upstream operations

DBTL-P

No description specified

Submitter: Konstantinos Pyrgakis

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Bioprocess design

Study: Bioprocess synthesis

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 16th Dec 2020 at 15:43

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