Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

AK144841 in Cutaneous Squamous Cell Carcinoma (cSCC)

ABSTRACT: AK144841 in Cutaneous Squamous Cell Carcinoma (cSCC)

PROVIDER: PRJNA352422 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR4896660.fastq.gz	Fastqsanger.gz
	SRR4896670.fastq.gz	Fastqsanger.gz
	SRR4896680.fastq.gz	Fastqsanger.gz
	SRR4896690.fastq.gz	Fastqsanger.gz
	SRR4896661.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 42

Similar Datasets

Epigenome analysis of cutaneous squamous cell carcinoma samples

Project description:Genome wide DNA methylation profiling in cutaneous squamous cell carcinoma. The Infinium MethylationEPIC BeadChips 850K has been used to interrogate DNA methylation changes. The cohort included 23 patients in total, with precursors of squamous cell carcinoma (actinic keratosis group) and with cSCC at different stages.

2019-12-12 | E-MTAB-8542 | biostudies-arrayexpress

COL11A1 mutations in cutaneous squamous cell carcinoma [WES]

Project description:Whole exome sequencing was used to identify frequent COL11A1 mutations in cutaneous squamous cell carcinoma (cSCC).

2021-07-23 | GSE179296 | GEO

Long non-coding RNAs in cutaneous squamous cell carcinoma

Project description:The expression of lncRNAs in cutaneous squamous cell carcinoma (cSCC) were determined with a commercially available microarray (Arraystar Inc.,Rockville, Maryland USA). The Arraystar human lncRNA Microarray V3.0 containing 30,586 LncRNAs and 26,109 coding transcripts (mRNAs) A total of three patients with cSCC were biopsied. A total of three control (non-lesional skin) were biopsied.

2016-04-13 | E-GEOD-74859 | biostudies-arrayexpress

Long non-coding RNAs in cutaneous squamous cell carcinoma

2016-04-13 | GSE74859 | GEO

Differential expression analysis of cutaneous squamous cell carcinoma and basal cell carcinoma proteomic profiles sampled with e-biopsy

Project description:Clinical misdiagnosis between cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC) affects treatment plans and carries risks of potential for recurrence, metastases, morbidity and mortality. We report the development of a novel tissue sampling approach with molecular biopsy using electroporation. This method, coined e-biopsy, enables non-destructive non-thermal permeabilization of cells in the skin for efficient vacuum-assisted extraction of informative biomolecules for rapid diagnosis. We used e-biopsy for ex vivo proteome extraction from 3 locations per patient in 21 cSCC and 20 BCC pathologically validated human tissue samples. The total 123 extracted proteomes were profiled using LC/MS/MS. The obtained mass spectra presented significantly different proteome profiles for cSCC and BCC with several hundreds of proteins significantly differentially expressed in each tumor in comparison to the other. Notably, our study showed that proteomes sampled with e-biopsy from cSCC and BCC lesions are different, and that 7 proteins were significantly overexpressed in BCC in comparison to cSCC even after the Bonferroni correction (FDR=7.1e-03). Our results provide evidence that the e-biopsy approach could potentially be used as a tool to support cutaneous tumors classification with rapid molecular profiling.

2024-08-22 | PXD046711 | Pride

Characterisation of the adhesome of patient-derived cutaneous squamous carcinoma cells

Project description:Interactions between cells and the extracellular matrix, mediated by integrin adhesion complexes (IACs), play key roles in cancer progression and metastasis. We report here systems-level changes in the adhesome during progression of a patient-derived cutaneous squamous cell carcinoma (cSCC). We found that the actin regulatory protein Mena is enriched in IACs in metastatic cSCC cells and is connected within a subnetwork of actin-binding proteins to the LINC complex component nesprin-2.

2023-03-25 | PXD021492 | Pride

Investigation of potential tumour suppressor or tumour promoter roles in cutaneous squamous cell carcinoma progression

Project description:Analysis of the combined dataset of normal skin, actinic keratosis and cutaneous squamous cell carcinoma (cSCC) previously submitted in (GSE45216) at genomic/transciptomic level. We identified potential cSCC driver genes significantly mutated and upregulated in cSCC relative to normal skin.

2018-06-14 | GSE98774 | GEO

RNA-Seq whole transcriptome analysis of normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines.

Project description:The incidence of keratinocyte-derived skin cancer, cutaneous squamous cell carcinoma (cSCC) is increasing worldwide making it the second most common metastatic skin cancer. In this project we used SOLiD next generation sequencing to characterize gene expression profiles in normal human epidermal keratinocytes (NHEKs) and cSCC cell lines. Total RNAs from normal human epidermal keratinocytes (NHEKs) (n=4) and cSCC cell lines (n=8) were extracted. The samples were sequenced using SOLiD next generation sequencing.

2015-08-27 | E-GEOD-66412 | biostudies-arrayexpress

Long Non-coding RNA PICSAR Promotes Growth of Cutaneous Squamous Cell Carcinoma by Regulating ERK1/2 Activity

Project description:Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. Long non-coding RNAs (lncRNAs) are involved in various biological processes, and their role in cancer progression is emerging. Whole transcriptome analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=4) revealed overexpression of long intergenic ncRNA (LINC00162) in cSCC cells (GSE66412). We wanted to futher study the RNA expression profile of LINC00162 knockdown cSCC cells. Based on our observations, LINC00162 was named PICSAR (P38 Inhibited Cutaneous Squamous cell carcinoma Associated lincRNA).

2016-08-31 | GSE77950 | GEO

Analysis of the gene expression profile in normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines

Project description:The incidence of keratinocyte-derived skin cancer, cutaneous squamous cell carcinoma (cSCC) is increasing worldwide making it the second most common metastatic skin cancer. We used microarrays to characterize gene expression profile in normal human epidermal keratinocytes (NHEK) and cSCC cell lines. Total RNAs from normal human epidermal keratinocytes (n=5) and cSCC cell lines (n=8) were extracted. The samples were processed for Affymetrix 3´ IVT Express Kit according to manufacture’s protocol.

2015-08-27 | E-GEOD-66359 | 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