Assays

What is an Assay?

1310 Assays visible to you, out of a total of 2286

Library Prep: Training Data - Metadata

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: Systems-level computational translation of mous...

Organisms: No organisms

SOPs: No SOPs

Data files: samples-publish_KPRF_DNA.xlsx, samples-publish_KPRF_RNA.xlsx, samples-publish_KPRF_TIS.xlsx

Snapshots: No snapshots

Created: 5th Feb 2025 at 18:28, Last updated: 5th Feb 2025 at 19:23

Tissue Collection: Training Data - Metadata

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: Systems-level computational translation of mous...

Organisms: No organisms

SOPs: No SOPs

Data files: samples-publish_KPRF_BAC.xlsx, samples-publish_KPRF_MUS.xlsx, samples-publish_KPRF_PAT.xlsx, samples-publish_KPRF_PAV.xlsx, samples-publish_KPRF_TIS.xlsx

Snapshots: No snapshots

Created: 5th Feb 2025 at 17:09, Last updated: 5th Feb 2025 at 19:06

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: Intravenous BCG-mediated protection against tub...

Organisms: No organisms

SOPs: No SOPs

Data files: A.DBMM-ASIVBCG.xlsx, samples-publishAS-BCG_A.DBMM, samples-publishAS-BCG_D.SEQ

Snapshots: No snapshots

Created: 23rd Jan 2025 at 20:37, Last updated: 3rd Feb 2025 at 22:38

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: Intravenous BCG-mediated protection against tub...

Organisms: No organisms

SOPs: P.FOR-230503-V1_Barcoding_Amplicon_Feb2023

Data files: samples-publishAS-BCG_D.SEQ, samples-publishAS-BCG_DNA

Snapshots: No snapshots

Created: 23rd Jan 2025 at 20:35, Last updated: 3rd Feb 2025 at 22:36

Library Prep - Metadata

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: Intravenous BCG-mediated protection against tub...

Organisms: No organisms

SOPs: P.FOR-230503-V1_Barcoding_Amplicon_Feb2023

Data files: samples-publishAS-BCG_BAC_extracted, samples-publishAS-BCG_DNA

Snapshots: No snapshots

Created: 23rd Jan 2025 at 20:23, Last updated: 3rd Feb 2025 at 22:27

Bacterial Extraction - Metadata

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: Intravenous BCG-mediated protection against tub...

Organisms: No organisms

SOPs: P.FOR-231011_Bacterial Extraction

Data files: samples-publishAS-BCG_BAC_extracted, samples-publishAS-BCG_TIS.xlsx

Snapshots: No snapshots

Created: 23rd Jan 2025 at 20:22, Last updated: 3rd Feb 2025 at 22:20

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: Intravenous BCG-mediated protection against tub...

Organisms: No organisms

SOPs: P.FLY-220823-V1_P---PET_CT_Imaging.docx

Data files: samples-publishAS-BCG_D.IMG.xlsx, samples-publishAS-BCG_PAV.xlsx

Snapshots: No snapshots

Created: 23rd Jan 2025 at 20:20, Last updated: 3rd Feb 2025 at 22:14

Tissue Collection - Metadata

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: Intravenous BCG-mediated protection against tub...

Organisms: No organisms

SOPs: P.FLY-250203-V1_IVBCG-AS-NHP-Protocol.docx

Data files: samples-publishAS-BCG_PAV.xlsx, samples-publishAS-BCG_TIS.xlsx

Snapshots: No snapshots

Created: 23rd Jan 2025 at 20:18, Last updated: 3rd Feb 2025 at 21:55

Flow Cytometry - Data Linked

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: Intravenous BCG-mediated protection against tub...

Organisms: No organisms

SOPs: No SOPs

Data files: samples-publishAS-BCG_TIS.xlsx

Snapshots: No snapshots

Created: 23rd Jan 2025 at 20:38, Last updated: 3rd Feb 2025 at 21:55

Patient Visit - Metadata

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: Intravenous BCG-mediated protection against tub...

Organisms: No organisms

SOPs: P.FLY-250203-V1_IVBCG-AS-NHP-Protocol.docx

Data files: samples-publishAS-BCG_AB.xlsx, samples-publishAS-BCG_BAC.xlsx, samples-publishAS-BCG_NHP.xlsx, samples-publishAS-BCG_PAV.xlsx

Snapshots: No snapshots

Created: 23rd Jan 2025 at 20:17, Last updated: 3rd Feb 2025 at 21:24

Microvascular Network Formation - Metadata

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-240712_V1_GFP_OOC-MVN_Protocol.docx

Data files: samples-publishGFP_CEL.xlsx, samples-publishGFP_CEL.xlsx, samples-publishGFP_OOC.xlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:31, Last updated: 28th Jan 2025 at 19:30

Microfluidic Device Imaging - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-240712_V1_GFP_Extravasation.docx

Data files: samples-publishGFP_D.IMG.xlsx, samples-publishGFP_OOC.xlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:33, Last updated: 28th Jan 2025 at 19:30

Influence of pH and HRT on xylan fermentation

Cell4Chem

(Show All)

No description specified

Submitter: Juan Iglesias-Riobó

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

Study: 1 hidden item

Organisms: No organisms

SOPs: No SOPs

Data files: Xylan_Batch_1, Xylan_CSTR_1, Xylan_SBR_1, Xylan_SBR_cycles

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.2157.1

Created: 6th Sep 2023 at 08:35, Last updated: 28th Jan 2025 at 14:29

Histology - Data Linked

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: Comparable Non-canonical T cell responses are a...

Organisms: No organisms

SOPs: P.SAS-250124-V1_Histology-Protocol.docx

Data files: samples-publishMP_RSTR-D.IMG.xlsx, samples-publishMP_RSTR-TIS.xlsx

Snapshots: No snapshots

Created: 23rd Jan 2025 at 21:13, Last updated: 24th Jan 2025 at 20:55

Flow Cytometry Analysis - Data Linked

Hi-IMPAcTB

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: Intravenous BCG-mediated protection against tub...

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 23rd Jan 2025 at 20:40

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: No SOPs

Data files: SH_AllMetadata_v2.xlsx

Snapshots: No snapshots

Created: 16th Jul 2024 at 16:55, Last updated: 15th Jan 2025 at 19:09

Library Prep - Metadata

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-240712_V1_GFP_RNAseq.docx

Data files: samples-publishGFP_DNA.xlsx, samples-publishGFP_RNA.xlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:38, Last updated: 15th Jan 2025 at 19:09

Short Read Sequencing - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-240712_V1_GFP_RNAseq.docx

Data files: samples-publishGFP_D.SEQ.xlsx, samples-publishGFP_DNA.xlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:39, Last updated: 15th Jan 2025 at 19:09

Real-time RT-PCR - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-240712_V1_GFP_rtPCR.docx

Data files: samples-publishGFP_D.PCRxlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:41, Last updated: 15th Jan 2025 at 19:09

Gene Expression Analysis - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-240712_V1_GFP_RNAseq.docx

Data files: samples-publishGFP_A.GEX.xlsx, samples-publishGFP_D.SEQ.xlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:41, Last updated: 15th Jan 2025 at 19:09

Fluorescence-Activated Cell Sorting - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-240712_V1_GFP_FACS.docx

Data files: samples-publishGFP_CEL.xlsx, samples-publishGFP_D.FLOW.xlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:35, Last updated: 15th Jan 2025 at 19:09

Cell Culture Imaging - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-240712_V1_GFP_Size-and-Proliferation.docx

Data files: samples-publishGFP_CEL.xlsx, samples-publishGFP_CEL.xlsx, samples-publishGFP_D.IMG.xlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:36, Last updated: 15th Jan 2025 at 19:09

Cell Culture Imaging Analysis - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-240712_V1_GFP_Size-and-Proliferation.docx

Data files: samples-publishGFP_A.CCI.xlsx, samples-publishGFP_D.IMG.xlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:37, Last updated: 15th Jan 2025 at 19:09

RNA Extraction - Metadata

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-240712_V1_GFP_RNAseq.docx

Data files: samples-publishGFP_CEL.xlsx, samples-publishGFP_RNA.xlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:37, Last updated: 15th Jan 2025 at 19:09

Cell Culture - Metadata

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-230131-V1_Cell-culture.docx, P.KAM-240712_V1_GFP_CellCulture.docx

Data files: samples-publishGFP_CEL.xlsx, samples-publishGFP_CEL.xlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:30, Last updated: 15th Jan 2025 at 19:09

Cancer Cell Extravasation Analysis - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Polyploidy of MDA-MB-231 cells drives increased...

Organisms: No organisms

SOPs: P.KAM-240712_V1_GFP_Extravasation.docx

Data files: samples-publishGFP_A.CCE.xlsx, samples-publishGFP_D.IMG.xlsx

Snapshots: No snapshots

Created: 12th Jul 2024 at 17:34, Last updated: 15th Jan 2025 at 19:09

Cell Culture and Tumor Spheroid Creation - Metadata

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Patient-specific vascularized tumor model: Bloc...

Organisms: No organisms

SOPs: P.KAM-230131-V1_Cell-culture.docx, P.KAM-240129-V1_Cell-Culture-and-Tumor-Spheroid..., P.KAM-240129-V1_Monocyte-Isolation-iVas.docx

Data files: samples-publish2024-02-09-CEL.xlsx

Snapshots: No snapshots

Created: 9th Feb 2024 at 17:54, Last updated: 15th Jan 2025 at 17:58

Python packages

Millar group

The list of python packages used was obtained by typing inside the Docker image

pip list -- format==columns > python_packages_pip_installed.txt

This list the version of packages installed as we have observed issues related to the use of the most current version of some python packaged for example scipy

Submitter: Uriel Urquiza Garcia

Biological problem addressed: Gene Expression

Investigation: Absolute units for proteins in Arabidopsis cloc...

Study: Reproducibility documentation

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 4th Oct 2022 at 08:48, Last updated: 19th Dec 2024 at 11:28

Gatway maps of genomic regions of clock genes

Millar group

Maps of cloned genes for rescuing selected clock mutants

Submitter: Uriel Urquiza Garcia

Assay type: Transformation

Technology type: Technology Type

Investigation: Absolute units for proteins in Arabidopsis cloc...

Study: Construction of NanoLUC-tagged plants

Organisms: Arabidopsis thaliana, Escherichia coli

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 21st Jan 2023 at 12:54, Last updated: 19th Dec 2024 at 11:28

promoter binding affinity calculations on the genome based on PBMs and EMA for CCA1 and LUX

Millar group

The promoter regions for clock genes that present a ChIP-seq signal were extracted from TAIR10 using costume python scripts using the gene list for Kamioka et al CCA1 or Daphne Ezer et al for LUX. The promoter was considered from the TSS of the gene until the annotated end of the upstream gene. Then, this region was scanned using the Energy Matrix derived using EMA working as a classifier for bound or unbound. After classification the calibrated PBM data calibrated using in vitro data was used ...

Submitter: Uriel Urquiza Garcia

Biological problem addressed: Model Analysis Type

Investigation: Absolute units for proteins in Arabidopsis cloc...

Study: Estimating DNA-binding affinities for Arabidops...

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: CCA1 PBM E-score data Franco-Zorrilla et al, CCA1 ensemble of matrices, CCA1 peaks from Kamioka et al, LUX E-scores data from Helfer et al, LUX ensemble of matrices, LUX peaks Ezer et al

Snapshots: No snapshots

Created: 25th Aug 2024 at 13:45, Last updated: 19th Dec 2024 at 11:28

(v.1.16.2)

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