Assays

MCAD-KO mice (C57BL/6J background) were exposed to three different conditions: "fed", "fasting", and "fasting + cold". In this study we determined the concentration of various CoA biosynthetic intermediates (including CoA) and the expression of CoA metabolic genes in liver tissue samples from these groups of mice.

Submitter: Christoff Odendaal

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Mitochondrial fatty acid oxidation in human liver

Study: Sequestration of CoA and adaptation of CoA meta...

Organisms: No organisms

SOPs: No SOPs

Data files: Mice CoA biosynthetic intermediates (Fig. 4C), Mice qPCR (Fig. 4E-F)

Snapshots: No snapshots

Created: 9th May 2025 at 15:22, Last updated: 16th May 2025 at 11:45

Computational model (in silico)

PoLiMeR - Polymers in the Liver: Metabolism and Regulation

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No description specified

Submitter: Christoff Odendaal

Biological problem addressed: Model Analysis Type

Investigation: Mitochondrial fatty acid oxidation in human liver

Study: Sequestration of CoA and adaptation of CoA meta...

Organisms: No organisms

Models: Model notebooks, odendaal4

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 9th May 2025 at 14:40, Last updated: 16th May 2025 at 11:45

HepG2 cells (in vitro)

PoLiMeR - Polymers in the Liver: Metabolism and Regulation

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The behaviour of a published MCAD-KO HepG2 cell line was compared to that of a wild-type HepG2 cell line in terms of the changes in acyl-CoA and acylcarnitine levels (measured by HILIC-MS/MS) and gene expression pertaining to CoA metabolism (characterised by qPCR). Additionally, the incorporation of label from stable isotope-labelled pantothenate (vitamine B5) was over 24 hours of exposure to an energetic stressor was also investigated.

Submitter: Christoff Odendaal

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Mitochondrial fatty acid oxidation in human liver

Study: Sequestration of CoA and adaptation of CoA meta...

Organisms: Homo sapiens (batch)

SOPs: No SOPs

Data files: HepG2 CoA labelling data, palmitate/no-glucose ..., HepG2 acyl-CoA measurements, palmitate/low-gluc..., HepG2 acyl-CoA measurements, palmitate/no-gluco..., HepG2 acyl-CoA/acylcarnitine measurements stati..., HepG2 acyl-CoA/acylcarnitine measurements stati..., HepG2 acylcarnitine measurements, palmitate/low..., HepG2 acylcarnitine measurements, palmitate/no-..., HepG2 qPCR statistical significance, palmitate/..., HepG2 qPCR statistical significance, palmitate/..., HepG2 qPCR, palmitate/low-glucose (Fig. S11), HepG2 qPCR, palmitate/no-glucose (Fig. S9)

Snapshots: No snapshots

Created: 9th May 2025 at 14:50, Last updated: 16th May 2025 at 11:45

All Metadata

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Confined cell migration along extracellular mat...

Organisms: No organisms

SOPs: No SOPs

Data files: All Metadata PF-IVM_v1.xlsx

Snapshots: No snapshots

Created: 15th May 2025 at 19:02, Last updated: 15th May 2025 at 19:03

Imaging Analysis - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Confined cell migration along extracellular mat...

Organisms: No organisms

SOPs: P.FRI-250515-V1_3DOpticalFlowAlgorithm.docx, P.FRI-250515-V1_IntravitalMircoscopyofTumorCell...

Data files: samples-publish_PF-IVM_A.IMG.xlsx, samples-publish_PF-IVM_D.IMG.xlsx

Snapshots: No snapshots

Created: 15th May 2025 at 18:36, Last updated: 15th May 2025 at 19:01

Intravital Microscopy

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Confined cell migration along extracellular mat...

Organisms: No organisms

SOPs: P.FRI-250515-V1_IntravitalMircoscopyofTumorCell...

Data files: samples-publish_PF-IVM_D.IMG.xlsx, samples-publish_PF-IVM_MUS.xlsx

Snapshots: No snapshots

Created: 15th May 2025 at 18:35, Last updated: 15th May 2025 at 18:58

Modeling - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Chromatin conformation, gene transcription, and...

Organisms: No organisms

SOPs: P.BAC-250424-V1_Modeling_ChromatinConformation.pdf

Data files: samples-publish_VB-CC_MDL.xlsx

Snapshots: No snapshots

Created: 24th Apr 2025 at 17:25, Last updated: 24th Apr 2025 at 18:07

All Metadata

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Chromatin conformation, gene transcription, and...

Organisms: No organisms

SOPs: No SOPs

Data files: All Metadata - VB_CC.xlsx

Snapshots: No snapshots

Created: 24th Apr 2025 at 18:04, Last updated: 24th Apr 2025 at 18:06

Chromatin Sequencing Analysis - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Chromatin conformation, gene transcription, and...

Organisms: No organisms

SOPs: P.BAC-250422-V1_Hi-C_ChromatinConformation.docx

Data files: samples-publish_VB-CC_A.CHRM.xlsx, samples-publish_VB-CC_D.SEQ.xlsx

Snapshots: No snapshots

Created: 24th Apr 2025 at 17:16, Last updated: 24th Apr 2025 at 18:04

Short Read Sequencing - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Chromatin conformation, gene transcription, and...

Organisms: No organisms

SOPs: P.BAC-250422-V1_Hi-C_ChromatinConformation.docx

Data files: samples-publish_VB-CC_D.SEQ.xlsx, samples-publish_VB-CC_DNA.xlsx

Snapshots: No snapshots

Created: 24th Apr 2025 at 17:15, Last updated: 24th Apr 2025 at 18:00

Library Creation - Metadata

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Chromatin conformation, gene transcription, and...

Organisms: No organisms

SOPs: P.BAC-250422-V1_Hi-C_ChromatinConformation.docx

Data files: samples-publish_VB-CC_CEL.xlsx, samples-publish_VB-CC_DNA.xlsx

Snapshots: No snapshots

Created: 24th Apr 2025 at 17:12, Last updated: 24th Apr 2025 at 17:55

Imaging Analysis - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Chromatin conformation, gene transcription, and...

Organisms: No organisms

SOPs: P.BAC-250422-V1_ChromatinElectronMicroscopy_Chr..., P.BAC-250422-V1_PWS_ChromatinConformation.docx, P.BAC-250422-V1_SMLM_ChromatinConformation.docx

Data files: samples-publish_VB-CC_A.IMG.xlsx, samples-publish_VB-CC_D.IMG.xlsx

Snapshots: No snapshots

Created: 24th Apr 2025 at 17:11, Last updated: 24th Apr 2025 at 17:52

Cell Imaging - Data Linked

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Chromatin conformation, gene transcription, and...

Organisms: No organisms

SOPs: P.BAC-250422-V1_ChromatinElectronMicroscopy_Chr..., P.BAC-250422-V1_PWS_ChromatinConformation.docx, P.BAC-250422-V1_SMLM_ChromatinConformation.docx

Data files: samples-publish_VB-CC_CEL.xlsx, samples-publish_VB-CC_D.IMG.xlsx

Snapshots: No snapshots

Created: 24th Apr 2025 at 17:10, Last updated: 24th Apr 2025 at 17:49

Cell Culture - Metadata

MetNet

No description specified

Submitter: Charles Demurjian

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Chromatin conformation, gene transcription, and...

Organisms: No organisms

SOPs: P.BAC-250422-V1_CellCulture_ChromatinConformati...

Data files: samples-publish_VB-CC_CEL.xlsx

Snapshots: No snapshots

Created: 24th Apr 2025 at 17:09, Last updated: 24th Apr 2025 at 17:41

Tissue Collection – Metadata

Hi-IMPAcTB

No description specified

Submitter: Dikshant Pradhan

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: Antibody-Fab and -Fc features promote Mycobacte...

Organisms: No organisms

SOPs: No SOPs

Data files: samples-publish_PG_MUS.xlsx, samples-publish_PG_TIS.xlsx

Snapshots: No snapshots

Created: 14th Mar 2022 at 17:15, Last updated: 23rd Apr 2025 at 19:35

Cell Extraction - Metadata

Hi-IMPAcTB

No description specified

Submitter: Dikshant Pradhan

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: IMPAcTB

Study: Antibody-Fab and -Fc features promote Mycobacte...

Organisms: No organisms

SOPs: P.ALT-241105-V1_Protocol_phagocytic_assays_BM_c..., P.ALT-250314-V1_scRNA_PG.docx, P.ALT-250418-V1_Protocol_mtb_restriction_assay_...

Data files: samples-publish_PG_CEL.xlsx, samples-publish_PG_TIS.xlsx

Snapshots: No snapshots

Created: 14th Mar 2022 at 17:16, Last updated: 23rd Apr 2025 at 19:35

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