Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis by RNAseq of the transcriptome of different stage of skin carcinogenesis induced by topical application of DMBA/TPA

ABSTRACT: Total RNA extracted from biopsies of healthy skin, papilloma, SCC Tumor and of 2 cell lines isolated from these tumors were purified using miRNeasy minikit (Qiagen). RNA libraries were then generated with the NEB next small library prep set for SOLID (New England Biolabs) and sequenced on the Applied Biosystems SOLiD 5500 wildfire system following the manufacturer's instructions.

ORGANISM(S): Mus musculus

PROVIDER: GSE89509 | GEO | 2017/06/07

SECONDARY ACCESSION(S): PRJNA352411

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Analysis of CAL165 cells transcriptome using RNASeq

Project description:Total RNA extracted from the head and neck cell line CAL165 were purified using miRNeasy minikit (Qiagen). RNA libraries were then generated with the NEB next small library prep set for SOLID (New England Biolabs) and sequenced on the Applied Biosystems SOLiD 5500 wildfire system following the manufacturer's instructions.

2017-06-07 | GSE89510 | GEO

Small RNA sequencing of mouse bone marrow derived extracellular vesicles [EV.sRNA]

Project description:Mouse BM extracellular vesicles were isolated from Ocn-GFP Topaz mice using the Exoeasy and miRneasy (Qiagen). Small RNA libraries were constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England biolabs). Libraries were sequenced using Hiseq2500 instrument

2021-12-08 | GSE127864 | GEO

Cell type-specific epigenomic analysis in the developing heart

Project description:The molecular mechanisms governing heart development provide an important framework to understand congenital heart disease. The embryonic vertebrate heart tube develops an atrioventricular canal that divides the atrial and ventricular chambers, forms atrioventricular conduction tissue and organizes valve development. To better understand the molecular mechanism underlying atrioventricular canal versus chamber myocardium expression, a double-reporter transgenic mouse line was generated in which the expression of EGFP (green fluorescent protein) and Katushka (red fluorescent protein) are selectively expressed in the atrioventricular canal and in the chamber myocardium, respectively. We assessed the genome-wide H3K27ac pattern in isolated embryonic AV canal and in chamber cardiomyocytes, respectively. EGFP and Katushka-positive cells were purified by FACS and fixed. ChIP was performed with the truemicro ChIP (Diagenode) according to the manufacturer’s protocol using the H3K27ac antibody (abcam ab4729). Chipped DNA were subjected to library preparation using the 5500 Series SOLiD™ Systems ample preparation kit (Applied Biosystems) according to manufactures recommendations and sequenced using the 5500 wildfire system (SOLiD).

2014-03-06 | E-GEOD-55611 | biostudies-arrayexpress

RNA-seq of cells in Mus musculus nasal turbinates with or without 7DW8-5 treatment

Project description:Total RNA from cells in nasal turbinate was extracted with miRNeasy micro kit (Qiagen, 217084) according to the manufacturer’s instructions. ERCC RNA Spike-In Mix kit (ThermoFisher Scientific, 4456740) was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina according to manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). The samples were sequenced by the Illumina HiSeq instrument according to manufacturer’s instructions using a 2x150bp Paired End (PE) configuration.

2023-06-27 | E-MTAB-12345 | biostudies-arrayexpress

Circulating Extracellular Vesicular MicroRNA Signatures in Early Gestation Show an Association with Subsequent Clinical Features of Pre-Eclampsia

Project description:We report the differential abundance of cell free miRNAs extracted from extracellular vesicles (EV) in the peripheral blood of pregnant women with or without preeclampsia by Next Generation Sequencing. Maternal blood samples were collected form pregnant women enrolled in the study during first to very early second trimester (11–14 weeks ), mid- to late second trimester (19–22 weeks), third trimester (36 weeks) and at delivery. Extracellular vesicles were isolated from peripheral blood and total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer’s instruction. miRNA libraries were prepared utilizing NEB Next Multiplex small RNA Library prep kit (NEB E7300S; New England Biolabs, Inc, Ipswich, MA, USA) and libraries were subsequently sequenced using the HiSeq-2500 platform with single-end 50bp reads (Illumina Inc.; San Diego, CA, USA).

2024-08-01 | GSE247251 | GEO

Integrative Epigenetic Analysis Reveals Therapeutic Targets to the DNA Methyltransferase Inhibitor SGI-110 in Hepatocellular Carcinoma Cells [methylation]

Project description:For the AcceSssIble assay, nuclei preparation and M.SssI methyltransferase (New England BioLabs) treatment were performed. The subsequent Infinium DNA methylation assay was performed at the University of Southern California Molecular Genomics Core Facility according to the manufacturer’s specifications (Illumina).

2018-06-26 | GSE105066 | GEO

Deletion of 14-3-3σ sensitizes mice to DMBA/TPA-induced papillomatosis.

Project description:The p53-inducible cell cycle regulator 14-3-3σ exhibits tumor suppressive functions and is highly expressed in differentiating layers of the epidermis and hair follicles. 14-3-3σ/SFN/stratifin is frequently silenced in human epithelial cancers, and experimental down-regulation of 14-3-3σ expression immortalizes primary human keratinocytes. In the repeated-epilation (ER) mouse model, a heterozygous nonsense mutation of 14-3-3σ causes repeated hair-loss, hyper-proliferative epidermis, and spontaneous development of papillomas and squamous cell carcinomas in aging mice. Therefore, loss of 14-3-3σ function might contribute to epithelial tumor development. Here, we generated mice with loxP sites surrounding the single 14-3-3σ exon which allowed Cre-mediated deletion of the gene. 14-3-3σ-deficient mice are viable, but demonstrate a permanently disheveled fur. However, histological analyses of the skin did not reveal obvious defects in the hair follicles or the epidermis. Deletion of 14-3-3σ did not enhance spontaneous epidermal tumor development, whereas it increased the frequency and size of DMBA/TPA-induced papillomas. In conclusion, 14-3-3σ is dispensable for normal epidermal homeostasis but critical for suppression of chemically-induced skin carcinogenesis. In addition, these results suggest that the ER mutation of 14-3-3σ is not equivalent to loss of 14-3-3σ, but may represent a gain-of-function variant, which does not reflect the organismal function of wild-type 14-3-3σ.

| S-EPMC5216908 | biostudies-literature

Genome-wide gene expression patterns in reprogramming MEF infected by SeVdp vectors carrying KLF4 WT or L507A mutant

Project description:To evaluate global gene expression pattern changes between KLF4 L507A and WT during reprogramming, RNA-Seq was performed on the samples collected from reprogramming MEF infected with SeVdp vectors carrying KLF4 WT or L507A mutant. Original MEF and resulting miPSCs (mouse iPSCs) were also used as samples. RNA-seq library was generated using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) and NEBNext rRNA Delepletion Kit (New England Biolabs) by Lab Droid “Maholo” (Robotic Biology Institute) automatically. Paired-end sequencing of the libraries was performed using Novaseq 6000 SP Sequencing system using SP 100 cycle kit (Illumina). Reads from RNA-seq experiments were mapped to the mouse genome (GRCm38 or mm10) and analyzed for differential gene expression and PCA (principal component analysis) using CLC Genomics Workbench (Qiagen) software.

2021-09-27 | GSE184449 | GEO

T-cell-expressed proprotein convertase FURIN inhibits DMBA/TPA-induced skin cancer development.

Project description:Proprotein convertases (PCSK) have a critical role in the body homeostasis as enzymes responsible for processing precursor proteins into their mature forms. FURIN, the first characterized member of the mammalian PCSK family, is overexpressed in multiple malignancies and the inhibition of its activity has been considered potential cancer treatment. FURIN has also an important function in the adaptive immunity, since its deficiency in T cells causes an impaired peripheral immune tolerance and accelerates immune responses. We addressed whether deleting FURIN from the immune cells would strengthen anticancer responses by subjecting mouse strains lacking FURIN from either T cells or macrophages and granulocytes to the DMBA/TPA two-stage skin carcinogenesis protocol. Unexpectedly, deficiency of FURIN in T cells resulted in enhanced and accelerated development of tumors, whereas FURIN deletion in macrophages and granulocytes had no effect. The epidermises of T-cell-specific FURIN deficient mice were significantly thicker with more proliferating Ki67+ cells. In contrast, there were no differences in the numbers of the T cells. The flow cytometric analyses of T-cell populations in skin draining lymph nodes showed that FURIN T-cell KO mice have an inherent upregulation of early activation marker CD69 as well as more CD4+CD25+Foxp3+ positive T regulatory cells. In the early phase of tumor promotion, T cells from the T-cell-specific FURIN knockout animals produced more interferon gamma, whereas at later stage the production of Th2- and Th17-type cytokines was more prominent than in wild-type controls. In conclusion, while PCSK inhibitors are promising therapeutics in cancer treatment, our results show that inhibiting FURIN specifically in T cells may promote squamous skin cancer development.

| S-EPMC5214164 | biostudies-literature

Loss of endogenous Nfatc1 reduces the rate of DMBA/TPA-induced skin tumorigenesis.

Project description:Immunosuppressive therapies using calcineurin inhibitors, such as cyclosporine A, are associated with a higher incidence of squamous cell carcinoma formation in mice and humans. Calcineurin is believed to suppress tumorigenesis in part through Nfatc1, a transcription factor expressed primarily in hair follicle bulge stem cells in mice. However, mice overexpressing a constitutively active Nfatc1 isoform in the skin epithelium developed increased spontaneous skin squamous cell carcinomas. Because follicular stem cells can contribute to skin tumorigenesis, whether the endogenous expression of Nfatc1 inhibits or enhances skin tumorigenesis is unclear. Here we show that loss of the endogenous expression of Nfatc1 suppresses the rate of DMBA/TPA-induced skin tumorigenesis. Inducible deletion of Nfatc1 in follicular stem cells before tumor initiation significantly reduces the rate of tumorigenesis and the contribution of follicular stem cells to skin tumors. We find that skin tumors from mice lacking Nfatc1 display reduced Hras codon 61 mutations. Furthermore, Nfatc1 enhances the expression of genes involved in DMBA metabolism and increases DMBA-induced DNA damage in keratinocytes. Together these data implicate Nfatc1 in the regulation of skin stem cell-initiated tumorigenesis via the regulation of DMBA metabolism.

| S-EPMC4603931 | biostudies-literature

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