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In vitro transcription studies used in a proof of concept whole transcriptome model predition study - MCF7 cells (2 of 4)

ABSTRACT: In vitro transcription studies used in a proof of concept whole transcriptome model predition study - MCF7 cells (2 of 4)

PROVIDER: PRJNA431291 | ENA |

REPOSITORIES: ENA

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In vitro transcription studies used in a proof of concept whole transcriptome model predition study

Project description:In vitro transcription studies used in a proof of concept whole transcriptome model predition study

| PRJNA431283 | ENA

In vitro transcription studies used in a proof of concept whole transcriptome model predition study - MCF7 cells (2 of 4)

Project description:MCF7 cells were exposed in triplicate to three agrichemicals for 24hrs at 8 concentrations and a DMSO vehicle control (0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10 μM plus DMSO vehicle controls). While a common set of DMSO controls was used, these CEL files were RMA normalized independently with each of the chemical treated groups. Gene expression was measured on an Affymetrix GeneTitan system. The compounds used were fenbuconazole (a.k.a FENB, CAS # 114369-43-6) a triazole fungicide, imazalil (a.k.a. IMAZ, CAS # 35554-44-0), an azole pesticide, and 2,4-dichlorophenoxyacetic acid (a.k.a. 2,4-D or 2-4-D in file names, CAS # 94-75-7), a chlorophenoxy herbicide.

2018-12-21 | GSE109509 | GEO

In vitro transcription studies used in a proof of concept whole transcriptome model predition study - HepG2 cells (4 of 4)

Project description:In vitro transcription studies used in a proof of concept whole transcriptome model predition study - HepG2 cells (4 of 4)

| PRJNA431290 | ENA

In vitro transcription studies used in a proof of concept whole transcriptome model predition study - A673 cells (1 of 4)

Project description:In vitro transcription studies used in a proof of concept whole transcriptome model predition study - A673 cells (1 of 4)

| PRJNA431288 | ENA

In vitro transcription studies used in a proof of concept whole transcriptome model predition study - HepaRG cells (3 of 4)

Project description:In vitro transcription studies used in a proof of concept whole transcriptome model predition study - HepaRG cells (3 of 4)

| PRJNA431292 | ENA

In vitro transcription studies used in a proof of concept whole transcriptome model predition study

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-12-21 | GSE109514 | GEO

In vitro transcription studies used in a proof of concept whole transcriptome model predition study - HepG2 cells (4 of 4)

Project description:HpeG2 cells were exposed in triplicate to three agrichemicals for 24hrs at 8 concentrations and a DMSO vehicle control (0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10 μM plus DMSO vehicle controls). While a common set of DMSO controls was used, these CEL files were RMA normalized independently with each of the chemical treated groups. Gene expression was measured on an Affymetrix GeneTitan system. The compounds used were fenbuconazole (a.k.a FENB, CAS # 114369-43-6) a triazole fungicide, imazalil (a.k.a. IMAZ, CAS # 35554-44-0), an azole pesticide, and 2,4-dichlorophenoxyacetic acid (a.k.a. 2,4-D or 2-4-D in file names, CAS # 94-75-7), a chlorophenoxy herbicide.

2018-12-21 | GSE109513 | GEO

In vitro transcription studies used in a proof of concept whole transcriptome model predition study - HepaRG cells (3 of 4)

Project description:HepaRG cells were exposed in triplicate to three agrichemicals for 24hrs at 8 concentrations and a DMSO vehicle control (0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10 μM plus DMSO vehicle controls). While a common set of DMSO controls was used, these CEL files were RMA normalized independently with each of the chemical treated groups. Gene expression was measured on an Affymetrix GeneTitan system. The compounds used were fenbuconazole (a.k.a FENB, CAS # 114369-43-6) a triazole fungicide, imazalil (a.k.a. IMAZ, CAS # 35554-44-0), an azole pesticide, and 2,4-dichlorophenoxyacetic acid (a.k.a. 2,4-D or 2-4-D in file names, CAS # 94-75-7), a chlorophenoxy herbicide.

2018-12-21 | GSE109511 | GEO

In vitro transcription studies used in a proof of concept whole transcriptome model predition study - A673 cells (1 of 4)

Project description:A673 cells were exposed in triplicate to three agrichemicals for 24hrs at 8 concentrations and a DMSO vehicle control (0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10 μM plus DMSO vehicle controls). While a common set of DMSO controls was used, these CEL files were RMA normalized independently with each of the chemical treated groups. Gene expression was measured on an Affymetrix GeneTitan system. The compounds used were fenbuconazole (a.k.a FENB, CAS # 114369-43-6) a triazole fungicide, imazalil (a.k.a. IMAZ, CAS # 35554-44-0), an azole pesticide, and 2,4-dichlorophenoxyacetic acid (a.k.a. 2,4-D or 2-4-D in file names, CAS # 94-75-7), a chlorophenoxy herbicide. CEL files with _Rep2 in their file name indicate arrays that were re-scanned due to technical issues with the initial instrument scan of the GeneTitan peg array.

2018-12-21 | GSE109508 | GEO

Exploring kidney allograft rejection: A proof-of-concept study using spatial transcriptomics

Project description:In this proof-of-concept study, spatial transcriptomics combined with public single-cell RNA sequencing data were used to explore the potential of this technology to study kidney allograft rejection. We aimed to map gene expression patterns within diverse pathological states by examining biopsies classified across non-rejection, T cell-mediated acute rejection, and interstitial fibrosis and tubular atrophy (IFTA). Our results revealed distinct immune cell signatures, including those of T and B lymphocytes, monocytes, mast cells, and plasma cells, and their spatial organization within the renal interstitium. We also mapped chemokine receptors and ligands to study immune-cell migration and recruitment. Finally, our analysis demonstrated differential spatial enrichment of transcription signatures associated with kidney allograft rejection across various biopsy regions. Interstitium regions displayed higher enrichment scores for rejection-associated gene expression patterns than did tubular areas, which had negative scores. This implies that these signatures are primarily driven by processes unfolding in the renal interstitium. Overall, this study highlights the value of spatial transcriptomics for revealing cellular heterogeneity and immune signatures in renal transplant biopsies, and demonstrates its potential for studying the molecular and cellular mechanisms associated with rejection. However, certain limitations must be borne in mind regarding the development and future applications of this technology.

2024-05-02 | GSE245870 | GEO

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