Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of mid-colon and mid-jejunum segments from C57BL/6J wild-type mice exposed to doxorubicin (DOX)

ABSTRACT: ADRs (adverse drug reactions) are one of the main reasons for treatment discontinuation or alterations in dose regimens in clinical settings. Chemotherapy-induced ADRs are common, especially gastrointestinal-induced ones. Within TransQST (transqst.org), one of the main goal is to improve the in vitro-in vivo translation in toxicological studies, as well as translation between non-clinical species (such as rat and mouse) and humans. This experimental setup therefore aimed to investigate the effects of DOX on mouse tissue derived from colon and jejunum biopsies. Experiments were conducted in a dose (5 and 10 mg/kg) and time series regimen (6, 24, 72 and 96h). Time-matched controls were measured as well. Intravenous exposure to DOX was performed with two doses (5 and 10 mg/kg), over a period of 4 days. Mucosal scrapes samples were collected for RNA isolation at 6, 24, 72 and 96h since initial exposure. Samples from time-matched controls (saline 10 mM Tris/NaOH buffer pH 8.5) were also quantified. This dataset is part of the TransQST collection.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Theo de Kok

PROVIDER: E-MTAB-11339 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Analysis of human healthy enteroids and colonoids (3D organoid models from small intestine and colon) exposed to chemotherapy agent Doxorubicin (DOX) sampled at four doses (1,10, 30 and 60uM) and three time points (24, 48 and 72h).

Project description:ADRs (adverse drug reactions) are one of the main reasons for treatment discontinuation or alterations in dose regimens in clinical settings. Chemotherapy-induced ADRs are common, especially gastrointestinal-induced ones. Within TransQST (transqst.org), one of the main goal is to improve the in vitro-in vivo translation in toxicological studies, as well as translation between non-clinical species (such as rat and mouse) and humans. This experimental setup therefore aimed to investigate the effects of DOX on 3D human organoid cultures derived from healthy small intestine and colon segments. Experiments were conducted in a dose (1,10, 30 and 60uM) and time series regimen (24, 48 and 72h). Time-matched controls (DMSO 0.1% and medium only) were measured as well. This dataset is part of the TransQST collection.

2022-01-27 | E-MTAB-11297 | biostudies-arrayexpress

Analysis of mouse healthy enteroids and colonoids (3D organoid models from small intestine and colon) exposed to chemotherapy agent Doxorubicin (DOX) sampled at four doses (0.1, 1, 10 and 30uM) and three time points (24, 48 and 72h).

Project description:ADRs (adverse drug reactions) are one of the main reasons for treatment discontinuation or alterations in dose regimens in clinical settings. Chemotherapy-induced ADRs are common, especially gastrointestinal-induced ones. Within TransQST (transqst.org), one of the main goal is to improve the in vitro-in vivo translation in toxicological studies, as well as translation between non-clinical species (such as rat and mouse) and humans. This experimental setup therefore aimed to investigate the effects of DOX on 3D mouse organoid cultures derived from healthy small intestine and colon segments. Experiments were conducted in a dose (0.1, 1, 10 and 30uM) and time series regimen (24, 48 and 72h). Time-matched controls (DMSO 0.1% and medium only) were measured as well. This dataset is part of the TransQST collection.

2022-12-31 | E-MTAB-11365 | biostudies-arrayexpress

Analysis of mid-colon and mid-jejunum segments from C57BL/6J wild-type mice exposed to 5-fluorouracil (5-FU). Intravenous exposure to 5-FU was performed with two doses (20 and 50 mg/kg), over a period of 4 days. Mucosal scrapes samples were collected for RNA isolation at 6, 24 and 96h since initial exposure. A recovery period of 2 days (sampled at 144h) followed up the 96h of repeated exposure. Samples from time-matched controls (saline 10 mM Tris/NaOH buffer pH 8.5) were also quantified.

Project description:ADRs (adverse drug reactions) are one of the main reasons for treatment discontinuation or alterations in dose regimens in clinical settings. Chemotherapy-induced ADRs are common, especially gastrointestinal-induced ones. Within TransQST (transqst.org), one of the main goal is to improve the in vitro-in vivo translation in toxicological studies, as well as translation between non-clinical species (such as rat and mouse) and humans. This experimental setup aimed to investigate the injury dynamics underlying repeated exposure to two doses of 5-FU (20 and 50 mg/kg), sampled at multiple time points (6, 24, 96 and 144h). The 144h time point comprises of recovery samples (i.e., 48h following the last dosing with 5-FU). This dataset is part of the TransQST collection.

2023-09-29 | E-MTAB-9120 | biostudies-arrayexpress

Analysis of human enteroids and colonoids (3D organoid models from small intestine and colon) exposed to chemotherapy agent and tyrosine kinase inhibitor (TKI) gefitinib sampled at four doses (0.1, 1, 10 and 30uM) and at three time points (24, 48 and 72h) since initial exposure

Project description:ADRs (adverse drug reactions) are one of the main reasons for treatment discontinuation or alterations in dose regimens in clinical settings. Chemotherapy-induced ADRs are common, especially gastrointestinal-induced ones. Within TransQST (transqst.org), one of the main goal is to improve the in vitro-in vivo translation in toxicological studies, as well as translation between non-clinical species (such as rat and mouse) and humans. This experimental setup therefore aimed to investigate the effects of gefitinib on 3D human organoid cultures derived from small intestine and colon segments. Experiments were conducted with a dose (0.1, 1, 10 and 30uM of gefitinib) and time series regimen (24, 48 and 72h). Time-matched controls (DMSO 0.1% and medium only) were also included. This dataset is part of the TransQST collection.

2022-04-11 | E-MTAB-11221 | biostudies-arrayexpress

RNA-seq of human colon biopsy tissue of healthy segments, from advanced breast cancer patients treated with capecitabine (5-FU)

Project description:ADRs (adverse drug reactions) are one of the main reasons for treatment discontinuation or alterations in dose regimens in clinical settings. Chemotherapy-induced ADRs are common, especially gastrointestinal-induced ones. Within TransQST (transqst.org), one of the main goal is to improve the in vitro-in vivo translation in toxicological studies, as well as translation between non-clinical species (such as rat and mouse) and humans. This experimental setup therefore aimed to investigate the effects of capecitabine, which is activated into 5-FU in the body, on advanced breast cancer patients. Healthy colon tissue was collected from the patients before and after the first cycle of the monotherapy, which consists of 2 weeks treatment followed by 1 week rest. Each patient was their own control sample. Transcriptomic data collected from the colon biopsies was compared with previous data collected from colon organoids to verify for the translatability of the in vitro model to humans. This dataset is part of the TransQST collaboration.

2022-08-01 | E-MTAB-11295 | biostudies-arrayexpress

Analysis of human enteroids and colonoids (3D organoid models from small intestine and colon) exposed to chemotherapy agent 5-fluorouracil (5FU) in a dose-repeated exposure across three doses (10,100 and 1000uM) and sampled at three points (24, 48 and 72h) since initial exposure. Organoids were obtained from healthy human tissues.

Project description:ADRs (adverse drug reactions) are one of the main reasons for treatment discontinuation or alterations in dose regimens in clinical settings. Chemotherapy-induced ADRs are common, especially gastrointestinal-induced ones. Within TransQST (transqst.org), one of the main goal is to improve the in vitro-in vivo translation in toxicological studies, as well as translation between non-clinical species (such as rat and mouse) and humans. This experimental setup therefore aimed to investigate the effects of 5FU on 3D human organoid cultures derived from small intestine and colon segments. Experiments were conducted in a dose-repeated (daily media refreshing with 10, 100 or 1000 uM of 5FU) and time series regimen (24, 48 and 72h). Time-matched controls (DMSO 0.1% and medium only) were measured, as well as a baseline exposure prior to the beginning of the exposures (medium only, 0h). This dataset is part of the TransQST collection.

2021-09-09 | E-MTAB-9134 | biostudies-arrayexpress

Analysis of mouse enteroids and colonoids exposed to chemotherapy agent 5-fluorouracil (5FU)

Project description:ADRs (adverse drug reactions) are one of the main reasons for treatment discontinuation or alterations in dose regimens in clinical settings. Chemotherapy-induced ADRs are common, especially gastrointestinal-induced ones. Within TransQST (transqst.org), one of the main goal is to improve the in vitro-in vivo translation in toxicological studies, as well as translation between non-clinical species (such as rat and mouse) and humans. This experimental setup therefore aimed to investigate the effects of 5FU on 3D mouse organoid cultures derived from small intestine and colon segments. Experiments were conducted in a dose-repeated (daily media refreshing with 10, 100 or 1000 uM of 5FU) and time series regimen (24, 48 and 72h). Time-matched controls (DMSO 0.1% and medium only) were measured, as well as a baseline exposure prior to the beginning of the exposures (medium only, 0h).

2023-09-29 | E-MTAB-9119 | biostudies-arrayexpress

Analysis of isotope incorporation in differentiated and undifferentiated podocytes

Project description:We subjected podocytes (either differentiated or undifferentiated) to a pulse with stable isotope labeled amino acids for 24, 48, 72 and 96h.

2018-05-01 | PXD006887 | Pride

APEX proximity labeling of murine NDUFS4 interacting proteins in podocytes

Project description:In this project we used an unbiased approach to identify the proteins that interact with NDUFS4 in the mouse podocytes using the APEX2 proximity labeling system. An immortalized murine podocyte was permanently transduced with a doxycycline (DOX) inducible NDUFS4-APEX2 chimeric construct. The cells were treated with DOX for 72 h to induce NDUFS4-APEX2 expression, followed by H2O2 activation of APEX2 mediated biotinylation of neighboring proteins. Biotinylated proteins were pull down by streptavidin beads and analyzed by LC-MS/MS. Cells without DOX induction or with DOX but without H2O2 activation were used as controls

2024-02-08 | PXD041378 | Pride

RNA-seq of murine small intestinal organoids treated with Ep300/Crebbp inhibitor I-CBP112 against untreated controls

Project description:Murine small intestinal organoids were cultured in the presence or absence of 3µM inhibitor I-CBP112 (PubChem CID 90488984), which targets E1A Binding Protein P300 (Ep300) and Creb-binding protein (Crebbp, Cbp). Organoids were grown in culture media containing EGF, Noggin and R-spondin (ENR), media was changed after 48h, and organoids were harvested after 96h.

2020-12-16 | E-MTAB-9290 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data