Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

51 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-Seq of human epithelial follicular cell line Nthy-ori 3-1 treated for 24 hours with benzo[a]pyrene or DMSO solvent control and mouse embryonic stem cell-derived thyroid follicles treated for 24 hours with DMSO solvent control.

ABSTRACT: The human epithelial follicular cell line Nthy-ori 3-1 was treated with 10 uM or 1 uM benzo[a]pyrene in 0.5% DMSO or with 0.5% DMSO only for 24 hours. Thyroid follicles were differentiated from a recombinant mESC line (A2LoxNkx2-1-Pax8) and treated with 0.5% DMSO for 24 hours. For Nthy-ori 3-1 samples, total RNA was extracted and used to prepare combined mRNA/miRNA libraries, poly(A) libraries and small RNA libraries. For thyroid follicles samples, total RNA was extracted and used to prepare combined mRNA/miRNA libraries.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER:

PROVIDER: E-MTAB-12078 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP140152

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-Seq of in vitro thyroid mouse organoids exposed to a dose range of phthalates for 24 hours. ATAC-Seq of human epithelial thryoid cell line Nthy-ori 3-1 exposed to DEHP or DINP (1 uM) for 5 days

Project description:Mouse RNA-Seq: cells derived from recombinant embryonic stem cell line (A2LoxNkx2-1-Pax8) were used. Mouse embryonic stem cell-derived thyroid follicles were exposed to a dose range of phthalates (DEHP, DIDP, DINP at 1-10-100 nM-1-10 uM; DnOP at 2-20-200 nM-2-20 uM) for 24 hours. Every condition was performed in triplicate. Untreated (n = 2) and 0.5% DMSO solvent (n = 5) controls were included. Combined mRNA/miRNA libraries were prepared and RNA-Seq performed. Human ATAC-seq: the human epithelial thyroid cell line, Nthy-ori 3-1, was exposed to DEHP or DINP for 5 days (n = 6), and ATAC-Seq was performed. 0.5% DMSO control samples (n = 6) were included.

2023-09-03 | E-MTAB-12830 | biostudies-arrayexpress

COPZ1 depletion in thyroid tumor cells triggers type-I IFN response and immunogenic cell death

Project description:Thyroid carcinoma (TC) is generally associated with good prognosis, nevertheless no effective treatments are available for aggressive forms not cured by current therapies. We previously identified the coatomer protein complex zeta 1 (COPZ1), as a new putative therapeutic target for TC, since its depletion impairs the viability of tumor cells, leads to abortive autophagy, ER stress, unfolded protein response and apoptosis, and reduces the tumor growth of TC xenograft models. In this study, by combining genomic, proteomic and functional approaches, we provided evidence that COPZ1 silencing stimulates a type I IFN-mediated viral mimicry response, boosts the production of several inflammatory molecules and finally induces immunogenic cell death, which, in turn, promotes dendritic cell maturation and subsequent activation of T cells. Collectively, our findings support the notion that COPZ1 targeting can be exploited as a new strategy to kill cancer cells with the subsequent involvement of an anti-tumor immune response.

2020-03-05 | PXD014423 | Pride

smalRNA seq of IPSC-cardiomyocytes treated with exosomes before hypoxic stiumli

Project description:This experiment aimed to investigate whether exosomess released by IPSC-cardiomyocytes during hypoxia can positively influence cardiac electrophysiology and miRNA expression during hypoxic stress. A multielectrode array (MEA) system was used as an in vitro method of recording real-time cardiac electrophysiological activity, highlighting the biological effects facilitated by exosomes. Additionally, miRNA-sequencing was performed to compare miRNA expressions in exosome-preconditioned and non-preconditioned IPSC-cardiomyocytes, elucidating important modulators of cardiac electrophysiology.

2024-04-01 | E-MTAB-13912 | biostudies-arrayexpress

RNA-seq of vastus lateralis muscle biopsies of newly diagnosed treatment-naïve NSCLC patients with cachexia and age-matched and sex-matched healthy controls

Project description:Cancer cachexia, highly prevalent in lung cancer, is a debilitating syndrome characterized by involuntary loss of skeletal muscle mass, and is associated with poor clinical outcome, decreased survival and negative impact on on tumor therapy. Here we sought to identify the muscle gene profile and pathways regulated in cachexia. Vastus lateralis muscle was obtained of newly diagnosed treatment-naïve NSCLC patients with cachexia (n = 8) and matched healthy controls (n = 8). Self-reported weight loss and body composition measurements defined cachexia status. RNA sequencing was performed on the Illumina NovasSeq 6000.

2023-04-03 | E-MTAB-12781 | biostudies-arrayexpress

RNA-seq of wild type (Hap), insulation (STITCH+30kb) and deletion (del(30-440)) of the MYC enhancer in human iPS cells.

Project description:We made insulation (STITCH+30kb) and deletion (del(30-440)) alleles of the MYC enhancer in human iPS cells. We employed RNA-seq to see how the insulation and deletion affects the transcriptome of the cells. We prepared libraries from three replicates for each configuration.

2020-05-01 | E-MTAB-7669 | biostudies-arrayexpress

Global gene expression analysis of H4T80A mutants vs WT H4 in Saccharomyces cerevisiae

Project description:Global RNA-seq gene expression analysis of H4T80A mutants vs WT H4 in Saccharomyces cerevisiae.

2018-09-05 | E-MTAB-7090 | biostudies-arrayexpress

Transcription profiling by array of human post-radiotherapy-induced thyroid tumors and sporadic counterparts to identify a discriminatory gene expression signature

Project description:Identification of a stable gene expression signature with high classifying potential to discriminate post-radiotherapy-induced thyroid tumors (follicular adenomas and papillary carcinomas) from their sporadic counterparts.

2010-08-01 | E-MEXP-2739 | biostudies-arrayexpress

In vitro RIP-seq for Zfp207 in mouse embryonic stem cells

Project description:in vitro RIP-seq assay of tagged Zfp207 performed in 2 technical replicates with Tag only and Input as negative controls. The input RNA used for the assay is total RNA extracted from mESC. The data provides information about the transcripts and the binding sites that Zfp207 has in the transcriptome of mESC

2021-12-09 | E-MTAB-10113 | biostudies-arrayexpress

Single cell RNA Sequencing (scRNA-Seq) on human embryonic stem cell-derived thyroid organoids exposed for 3 days to sex hormones + 1 day to benzo[a]pyrene (BaP) or PCB153

Project description:Human embryonic stem cell-derived thyroid follicles were exposed for 3 days to a mixture of the sex hormones beta-estradiol (E2), 5-alpha-dihydrotestosterone (DHT) and progesterone (PG) that resemble the serum levels of human male and female (post-ovulation) of reproductive age. Afterwards, they were exposed for 1 day to the mixtures of sex hormones + 10 uM benzo[a]pyrene (BaP) or 10 uM PCB153. At the end of the treatment period, organoids were dissociated into single cell suspension and single cell RNA-Sequencing (scRNA-Seq) performed.

2024-08-29 | E-MTAB-13502 | biostudies-arrayexpress

5hmC capture-seq of human monocytes and human monocyte-derived cells

Project description:We performed 5'-hydroxymethylcytosine (5hmC) capture sequencing to study the dynamics of 5hmC deposition during monocyte differentiation

2021-02-03 | E-MTAB-9928 | 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