Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV18 E7

ABSTRACT: Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV18 E7

PROVIDER: PRJNA631506 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11746175_1.fastq.gz	Fastqsanger.gz
	SRR11746175_2.fastq.gz	Fastqsanger.gz
	SRR11746176_1.fastq.gz	Fastqsanger.gz
	SRR11746176_2.fastq.gz	Fastqsanger.gz
	SRR11746177_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV18 E7

Project description:This RNA-seq study in primary human forekin keratinocytes was to define genes that are differetially expressed in the presence or absence of HPV18 E7 or the HPV18 E7 R84S variant.

2020-06-09 | GSE150201 | GEO

Analysis of gene expression in primary human foreskin keratinocytes +/- HPV16 E7 or PTPN14 knockout

Project description:This RNA-seq study in primary human forekin keratinocytes was to define genes that are differetially expressed in the presence or absence of HPV16 E7 or several HPV16 E7 variants. We also generated and conducted RNA-seq on primary human foreskin keratinocytes that were CRISPR-Cas9 edited with nontargeting sgRNA or sgRNA targeting PTPN14.

2019-02-28 | GSE121906 | GEO

Transcription profiling of human foreskin keratinocytes expressing E6 or E7 compared to normal keratinocytes reveals HPV16 E7 induces EMT

Project description:Gene expression data from human foreskin keratinocytes expressing E6 or E7 compared to normal keratinocytes.

2009-06-04 | E-MTAB-114 | biostudies-arrayexpress

Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV16 E7

2022-10-31 | GSE208280 | GEO

Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV16 E7

Project description:Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV16 E7

| PRJNA859114 | ENA

Analysis of gene expression in primary human foreskin keratinocytes +/- HPV16 E7 or PTPN14 knockout

Project description:Analysis of gene expression in primary human foreskin keratinocytes +/- HPV16 E7 or PTPN14 knockout

| PRJNA499044 | ENA

The impact of HPV16 and HPV18 E6/E7 oncogenes on gene expression in non-tumorigenic keratinocytes (HaCaT cells)

Project description:This analysis aimed to identify differentially expressed genes in non-tumorigenic keratinocytes transduced with E6/E7 oncogenes of HPV16 or 18. The working cell models were named HaCaT E6/E7 HPV16, HaCaT E6/E7 HPV18, and HaCaT pLVX (empty lentiviral vector) as controls. mRNA sequencing was performed on the Illumina NovaSeq 6000 platform by Novogene Bioinformatics Technology Co., Ltd, Beijing, China, with two independent replicate sequences for each cell model. Methodology: The bioinformatics pipeline analysis was executed as described below: Rstudio (v2023.06.1+524) and Galaxy (https://www.usegalaxy.orgaccessed on 15 August 2023) open-source platforms were used to analyze the Illumina raw data. The Quality Check was performed through the FastQC tool (v0.12.1); afterward, all the reads were processed by the Rsubread package (v2.14.2); at that point, the reads were trimmed and aligned to the Human Genome Reference (GRCh38.p14 v43). The resulting output was the BAM files, of which the number of reads was counted by the featureCounts tool (v2.0.3); at the final step, the Differential Expression Analysis was settled by DESeq2 tool (v2.11.40.8). The differential gene expression measurements were normalized by DESeq2´s median of ratios (median of ratio of gene counts relative to geometric mean per gene) method. All chemokine genes with an adjusted p-value (adj p) ≤ 0.05 and fold change (Log2FC) > 1 .5 or < -1.5 were selected as differentially expressed genes (DEGs). Some genes from the resulting outputs were validated through qPCR. Conclusions: Our study found 3296 differentially expressed genes in HaCaT E6/E7 HPV16 and 1943 in HaCaT E6/E7 HPV18. These results suggest that E6/E7 oncogenes from HPV16 and 18 can broadly modify transcriptomic expression.

2023-11-02 | GSE241704 | GEO

Expression signatures and cytogenetic aberrations in HPV16 E6, E7 and E6/E7-positive immortalized human epithelial cells

Project description:Identification of genetic/cytogenetic alterations and differentially expressed cellular genes in HPV16 E6, E7 and E6/E7 positive human foreskin keratinocytes Keywords: ordered We used microarrays to identify differentially expressed genes in human foreskin keratinocytes (HFK) transfected with retroviral vectors harboring the human papillomavirus type 16 oncogenes E6, E7, or E6/E7 in comparison to HFK containing the empty vector control pLXSN.

2013-11-27 | E-GEOD-14051 | biostudies-arrayexpress

Expression signatures and cytogenetic aberrations in HPV16 E6, E7 and E6/E7-positive immortalized human epithelial cells

Project description:Identification of genetic/cytogenetic alterations and differentially expressed cellular genes in HPV16 E6, E7 and E6/E7 positive human foreskin keratinocytes Keywords: ordered

2013-11-27 | GSE14051 | GEO

Gene expression of cervical cells and immortalized keratinocytes transfected with whole genomes of HPV16 and HPV18

Project description:Human ectocervical and endocervical cells immortalized by HPV16 E6/E7 (designated as Ect and End, respectively) and normal human immortalized keratinocytes (NIKS), were transfected with whole genomes of HPV16 or HPV18, and were subsequently grown in standard monolayer culture until passage 2. Total RNAs were extracted and subjected to TORAY 3D-gene analysis service using the 3D-Gene Human Oligo chip 25K (TORAY, Tokyo, Japan).

2019-08-01 | GSE131076 | GEO

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