Assays

What is an Assay?

1319 Assays visible to you, out of a total of 2303

Luminex - Data Linked

Endometriosis

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Endometriosis

Study: Organoid co-culture model of the cycling human ...

Organisms: No organisms

SOPs: No SOPs

Data files: samples-publish2023-11-03_CEL.xlsx, samples-publish2023-11-03_D.LMX.xlsx

Snapshots: No snapshots

Created: 3rd Nov 2023 at 15:11, Last updated: 17th Nov 2023 at 21:20

Elisa - Data Linked

Endometriosis

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Endometriosis

Study: Organoid co-culture model of the cycling human ...

Organisms: No organisms

SOPs: P.GRI-231103-V1_ELISA_Luminex_Protocol

Data files: samples-publish2023-11-03_CEL.xlsx, samples-publish2023-11-03_D.ELISA.xlsx

Snapshots: No snapshots

Created: 3rd Nov 2023 at 15:13, Last updated: 17th Nov 2023 at 21:20

Cell Culture Imaging - Data Linked

Endometriosis

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Endometriosis

Study: Organoid co-culture model of the cycling human ...

Organisms: No organisms

SOPs: P.GRI-231030-V4_Imaging_Protocol

Data files: samples-publish2023-11-03_AB_IMF.xlsx, samples-publish2023-11-03_CEL.xlsx, samples-publish2023-11-03_D.IMG_CCI.xlsx

Snapshots: No snapshots

Created: 3rd Nov 2023 at 15:14, Last updated: 17th Nov 2023 at 21:20

Short Read Sequencing - Data Linked

Endometriosis

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Endometriosis

Study: Organoid co-culture model of the cycling human ...

Organisms: No organisms

SOPs: P.GRI-231101-V1_RNA-isolation-and-bulk-RNA-seq

Data files: samples-publish2023-11-03_D.SEQ_CEL.xlsx, samples-publish2023-11-03_DNA_2.xlsx

Snapshots: No snapshots

Created: 3rd Nov 2023 at 18:29, Last updated: 17th Nov 2023 at 21:20

Patient Visit - Metadata

Endometriosis

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Endometriosis

Study: Organoid co-culture model of the cycling human ...

Organisms: No organisms

SOPs: P.GRI-230228-V1_2.1-Study-Approval.docx

Data files: samples-publish2023-11-03_PAT.xlsx, samples-publish2023-11-03_PAV.xlsx

Snapshots: No snapshots

Created: 3rd Nov 2023 at 14:08, Last updated: 17th Nov 2023 at 21:20

Tissue Collection - Metadata

Endometriosis

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Endometriosis

Study: Organoid co-culture model of the cycling human ...

Organisms: No organisms

SOPs: P.GRI-230228-V1_2.1-Study-Approval.docx, P.GRI-231030-V1_Tissue_Protocol

Data files: samples-publish2023-11-03_PAV.xlsx, samples-publish2023-11-03_TIS.xlsx

Snapshots: No snapshots

Created: 3rd Nov 2023 at 14:26, Last updated: 17th Nov 2023 at 21:20

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: CD8+ lymphocytes are critical for early control...

Organisms: No organisms

SOPs: No SOPs

Data files: All Metadata - CD8 Depletion.xlsx

Snapshots: No snapshots

Created: 13th Oct 2023 at 20:11, Last updated: 24th Oct 2023 at 16:40

Immunohistochemistry - Data Linked

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: CD8+ lymphocytes are critical for early control...

Organisms: No organisms

SOPs: P.FLY-230911-V1_IHC-CD8 Depletion

Data files: AB-IHC-samples-publish2023-10-11_17-10.xlsx, D.IMG-IHC-samples-publish2023-10-11_17-30.xlsx, TIS-samples-publish2023-10-11_14-11.xlsx

Snapshots: No snapshots

Created: 11th Oct 2023 at 16:48, Last updated: 23rd Oct 2023 at 20:08

PET/CT Scan - Data Linked

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: CD8+ lymphocytes are critical for early control...

Organisms: No organisms

SOPs: P.FLY-230523-V1_PET_CT_Imaging

Data files: D.IMG-PET-samples-publish2023-10-11_17-42.xlsx, PAV-2-samples-publish2023-10-11_13-11.xlsx

Snapshots: No snapshots

Created: 11th Oct 2023 at 16:46, Last updated: 23rd Oct 2023 at 19:33

Single Cell Expression Analysis - Data Linked

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: CD8+ lymphocytes are critical for early control...

Organisms: No organisms

SOPs: P.SHA-220912-V1_Drop-seq_Alignment_Cookbook.pdf

Data files: A.SCXP-samples-publish2023-10-11_18-00.xlsx, DSEQ-TIS-samples-publish2023-10-11_15-50.xlsx

Snapshots: No snapshots

Created: 11th Oct 2023 at 17:49, Last updated: 20th Oct 2023 at 19:30

Short Read Sequencing - Data Linked

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: CD8+ lymphocytes are critical for early control...

Organisms: No organisms

SOPs: P.FOR-230503-V1_Barcoding-Whole-Genome-Sequenci..., P.FOR-230503-V1_Barcoding_Amplicon_Feb2023, P.SHA-220819-V1_SeqWellHughes.et.al.Master.Prot...

Data files: DNA-BAC-samples-publish2023-10-11_14-51.xlsx, DNA-TIS-samples-publish2023-10-11_14-50.xlsx, DSEQ-BAC-samples-publish2023-10-11_15-51.xlsx, DSEQ-TIS-samples-publish2023-10-11_15-50.xlsx

Snapshots: No snapshots

Created: 11th Oct 2023 at 17:45, Last updated: 20th Oct 2023 at 19:27

Digitally Barcoded Mtb Matrix Analysis - Data Attached

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: CD8+ lymphocytes are critical for early control...

Organisms: No organisms

SOPs: P.FOR-231020-V1_DBMM-Analysis-CD8.docx

Data files: A.DBMM-samples-publish2023-10-11_16-10.xlsx, CD8 Depletion Digitally Barcoded MTB Matrix.xlsx, DSEQ-BAC-samples-publish2023-10-11_15-51.xlsx

Snapshots: No snapshots

Created: 11th Oct 2023 at 17:48, Last updated: 20th Oct 2023 at 19:27

DNA Extraction - Metadata

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: CD8+ lymphocytes are critical for early control...

Organisms: No organisms

SOPs: P.FOR-230503-V1_Barcoding_Amplicon_Feb2023, P.SHA-220819-V1_SeqWellHughes.et.al.Master.Prot...

Data files: BAC-samples-publish2023-10-11_14-35.xlsx, DNA-BAC-samples-publish2023-10-11_14-51.xlsx, DNA-TIS-samples-publish2023-10-11_14-50.xlsx, TIS-samples-publish2023-10-11_14-11.xlsx

Snapshots: No snapshots

Created: 11th Oct 2023 at 16:52, Last updated: 20th Oct 2023 at 16:00

Flow Cytometry - Data Linked

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: CD8+ lymphocytes are critical for early control...

Organisms: No organisms

SOPs: P.FLY-230509-V1_CD8-NX-Protocol

Data files: AB-FCS-samples-publish2023-10-11_15-07.xlsx, ABP-samples-publish2023-10-11_16-15.xlsx, D.FLOW-samples-publish2023-10-11_16-20.xlsx, TIS-samples-publish2023-10-11_14-11.xlsx

Snapshots: No snapshots

Created: 11th Oct 2023 at 16:49, Last updated: 20th Oct 2023 at 14:51

Flow Cytometry Analysis - Data Attached

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: CD8+ lymphocytes are critical for early control...

Organisms: No organisms

SOPs: No SOPs

Data files: A.FLOW-samples-publish2023-10-11_16-45.xlsx, CD8 counts AFLOW, CD8 cytokine AFLOW, D.FLOW-samples-publish2023-10-11_16-20.xlsx

Snapshots: No snapshots

Created: 11th Oct 2023 at 16:51, Last updated: 20th Oct 2023 at 14:51

Bacterial Extraction - Metadata

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: CD8+ lymphocytes are critical for early control...

Organisms: No organisms

SOPs: P.FOR-231011_Bacterial Extraction

Data files: BAC-samples-publish2023-10-11_14-35.xlsx, TIS-samples-publish2023-10-11_14-11.xlsx

Snapshots: No snapshots

Created: 11th Oct 2023 at 17:46, Last updated: 19th Oct 2023 at 18:25

Proteomic analyses

Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum

No description specified

Submitter: Lars Wöhlbrand

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Heat stress response of Prorcentrum cordatum

Study: Heat stress response of Prorocentrum cordatum

Organisms: No organisms

SOPs: No SOPs

Data files: 2D LC MS/MS peptide analyses, Membrane protein enriched fraction, Shotgun proteomic data

Snapshots: No snapshots

Created: 8th Jul 2022 at 13:19, Last updated: 16th Oct 2023 at 09:50

Metabolite analyses

Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum

No description specified

Submitter: Lars Wöhlbrand

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Heat stress response of Prorcentrum cordatum

Study: Heat stress response of Prorocentrum cordatum

Organisms: No organisms

SOPs: No SOPs

Data files: GCMS metabolite data

Snapshots: No snapshots

Created: 8th Jul 2022 at 13:27, Last updated: 16th Oct 2023 at 09:50

MolecularFormula Strings Spreadsheet_Ty

NMTrypI - New Medicines for Trypanosomatidic Infections

No description specified

Submitter: Pasquale Linciano

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Phenotypic and machine learning approaches for ...

Study: Ty-Box chemical characterization, properties an...

Organisms: No organisms

SOPs: No SOPs

Data files: Molecular Formula STRING

Snapshots: No snapshots

Created: 13th Oct 2023 at 07:12, Last updated: 13th Oct 2023 at 07:15

Molecular Formula STRING excel

NMTrypI - New Medicines for Trypanosomatidic Infections

No description specified

Submitter: Pasquale Linciano

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Phenotypic and machine learning approaches for ...

Study: Chemical characterization, and biological evalu...

Organisms: No organisms

SOPs: No SOPs

Data files: Molecular Formula STRING, Molecular Formula STRING

Snapshots: No snapshots

Created: 7th Oct 2023 at 16:57, Last updated: 7th Oct 2023 at 16:59

Usage of fine-tuned BioBERT for identification of chemical entities

BioCreative VII

Usage of fine-tuned BioBERT for identification of chemical entities

Submitter: Olga Krebs

Biological problem addressed: Annotation

Investigation: Chemical Identification and Indexing in PubMed ...

Study: Chemical named entity recognition and annotation

Organisms: No organisms

Models: WELT code

SOPs: No SOPs

Data files: BioCreative VII Track 2 - NLM-CHEM

Snapshots: No snapshots

Created: 12th Oct 2021 at 17:14, Last updated: 27th Sep 2023 at 14:21

Using semantic search in MesH and PubChem databases for entity linking

BioCreative VII

Using semantic search in MesH and PubChem databases for entity linking

Submitter: Olga Krebs

Biological problem addressed: Annotation

Investigation: Chemical Identification and Indexing in PubMed ...

Study: Chemical named entity recognition and annotation

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: BioCreative VII Track 2 - NLM-CHEM

Snapshots: No snapshots

Created: 12th Oct 2021 at 17:16, Last updated: 27th Sep 2023 at 14:21

Instructions for ENA submission

FAIRDOM, MESI-STRAT

Here we present ENA-requirements compliant template and SOP for submission steps

Submitter: Olga Krebs

Assay type: Transcriptomics

Technology type: Technology Type

Investigation: MESI-STRAT data for submission into public re...

Study: Sequence data for European Nucleotide Archive (...

Organisms: No organisms

SOPs: Standard Operating Procedure (SOP) for integra...

Data files: Excel template for metadata required by ENA t...

Snapshots: No snapshots

Created: 27th Sep 2023 at 13:56

GC-MS based analysis of metabolites

Adaptation of Salmonella enterica

No description specified

Submitter: Meina Neumann-Schaal

Assay type: Experimental Assay Type

Technology type: Gas Chromatography Mass Spectrometry

Investigation: Salmonella enterica relies on carbon metabolism...

Study: Metabolic analysis of Salmonella enterica to st...

Organisms: No organisms

SOPs: No SOPs

Data files: Salmonella enterica_metabolite data

Snapshots: Snapshot 1

Created: 21st Mar 2023 at 07:07, Last updated: 28th Aug 2023 at 13:57

Field Water Sensor Run

MIT SRP

No description specified

Submitter: Jake Schissel

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MIT SRP

Study: Benthic fluxes of fluorescent dissolved organic...

Organisms: No organisms

SOPs: P.HEM-220913-V2_20210513_fieldworkOperatingProc..., P.HEM-220913-V2_20210520_fieldworkOperatingProc..., P.HEM-220913-V2_20210610_fieldworkOperatingProc...

Data files: D.SNSR-samples-publish2022-10-11_18-50.xlsx, LOC-samples-publish2022-10-11_18-37.xlsx, bedford2_v2.zip, mystic9_v2.zip, sunder1_v2.zip

Snapshots: No snapshots

Created: 11th Oct 2022 at 13:51, Last updated: 18th Aug 2023 at 17:52

Inhibition of glycolytic flux

Whole body modelling of glucose metabolism in malaria patients

Inhibition of lactate flux glycolytic inhibitors

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Investigation: Glucose metabolism in Plasmodium falciparum inf...

Study: Analysis of model for malaria-infected erythroc...

Organisms: Plasmodium falciparum

Models: Glycolytic target analysis in malaria infected ..., Inhibition of glycolytic flux by glucose transp..., Kinetic model for steady state (dutoit1), Validation of lactate flux inhibition by glucos...

SOPs: No SOPs

Data files: Glycolytic flux inhibition data (erythrocytes), Lactate flux inhibition data

Snapshots: No snapshots

Created: 17th Apr 2023 at 12:26, Last updated: 18th Aug 2023 at 08:21

Flux vs external glucose

Whole body modelling of glucose metabolism in malaria patients

No description specified

Submitter: Dawie van Niekerk

Biological problem addressed: Validation

Investigation: Glucose metabolism in Plasmodium falciparum inf...

Study: Validation of model for malaria-infected erythr...

Organisms: Plasmodium falciparum

Models: Flux vs glucose, Kinetic model for infected red blood cell cultu...

SOPs: No SOPs

Data files: Flux vs glucose

Snapshots: No snapshots

Created: 17th Apr 2023 at 12:21, Last updated: 18th Aug 2023 at 07:59

Whole body modelling of glucose metabolism in malaria patients

No description specified

Submitter: Dawie van Niekerk

Biological problem addressed: Validation

Investigation: Glucose metabolism in Plasmodium falciparum inf...

Study: Validation of model for malaria-infected erythr...

Organisms: Plasmodium falciparum

Models: Kinetic model for steady state (dutoit1), Steady state (trophozoite stage)

SOPs: No SOPs

Data files: Stage specific fluxes

Snapshots: No snapshots

Created: 17th Apr 2023 at 12:18, Last updated: 18th Aug 2023 at 07:45

Malaria parasite volume determinations

Whole body modelling of glucose metabolism in malaria patients

Determinations of parasite volumes in a well-synchronised, infected culture treated with a cytosolic stain, using fluorescence microscopy. Diameters used to calculate parasite volume, assuming a spherical parasite cell.

Submitter: Dawie van Niekerk

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Glucose metabolism in Plasmodium falciparum inf...

Study: Intra-erythrocytic malaria parasite volumes

Organisms: No organisms

SOPs: No SOPs

Data files: Malaria parasite volumes determined using micro...

Snapshots: No snapshots

Created: 18th Aug 2023 at 07:26, Last updated: 18th Aug 2023 at 07:31

How to use templates for FAIR experimental data representation

Kinetics on the move - Workshop 2016

Here we will use JERM templates with embedded ontologies to describe and annotate example data

Submitter: Olga Krebs

Assay type: Interactomics

Technology type: Technology Type

Investigation: Using SEEK and I-S-A structure to integrate ex...

Study: Experimental study for hands on session

Organisms: No organisms

SOPs: Extraction and quantitative analysis of protein...

Data files: Master template, Transcriptomics Template (ArrayExpress Format)

Snapshots: No snapshots

Created: 27th May 2016 at 11:38, Last updated: 3rd Aug 2023 at 09:45

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