Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiRNA-seq analysis of RNA-binding protein knock-down HNSCC cell-line UMSCC74B

ABSTRACT: Purpose: The goals of this study is to compare NGS-derived miRNA profiling (miRNA-seq) of WT and FXR1 KD UMSCC74B cell-line Methods: miRNA profiles of UMSCC74B HNSCC cells treated with shControl(WT) and shFXR1 (KD), in duplicate, using Illumina hiseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks

ORGANISM(S): Homo sapiens

PROVIDER: GSE117031 | GEO | 2020/01/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Quantitative Analysis of Wild Type and Pich-KO fetal liver LSK Transcriptomes

Project description:mRNA profiles of embryonic day 14.5 wild-type (WT) and Pich-KO mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2022-03-09 | GSE188359 | GEO

Next Generation Sequencing Facilitates Analysis of Wild Type and glioma Transcriptomes

Project description:Methods: Brain mRNA profiles of 90-day-old wild-type (WT) and glioma were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2021-03-16 | GSE129899 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and KRAS mutated lung oraganoids Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare lung organoids transcriptome profiling (RNA-seq) between wild type and KRAS mutation Methods: mRNA profiles of wild-type (WT) and KRAS mutated organoids were generated by deep sequencing, in triplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2023-06-01 | GSE171728 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Osmr-/- Epidermal keratinocytes Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare epidermal keratinocytes transcriptome profiling (RNA-seq) between wild type and Osmr-/- mice Methods: Epidermal keratinocytes mRNA profiles of wild-type (WT) and Oncostatin M receptor (Osmr−/−) mice were generated by deep sequencing, in triplicate. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2021-03-18 | GSE150884 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of HePG2i cell line with and without DOX induced GATA4 expression Transcriptomes

Project description:HePG2i cell line mRNA profiles of DOX induced GATA4 expression and non-DOX induced were generated by deep sequencing, in triplicate, using Illumina HiSeq 10000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2019-08-09 | GSE135579 | GEO

Next generation sequencing facilitates quantitative analysis of colonic tissue from miR-7 deficiency and WT mice with IBD mice, and human colonic epithelial cells transfected-with NC/miR-7 inhibitor/miR-7 inhibitor plus Erlotinib following LPS treatment

Project description:Methods: Colon tissue from 8-10-Week wild-type (WT) and miR-7 deficiency mice with DSS treatment, and miR-7 inhibitor/NC-transfected-FHC cells and Erlotinib plus miR-7 inhibitor-transfected-FHC cells with LPS treatment, mRNA profiles of which were generated by deep sequencing, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

2023-06-30 | GSE174331 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Retinoblastoma Transcriptomes

Project description:Methods: mRNA profiles of retinoblastoma samples and para-tumor were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

2018-02-28 | GSE111168 | GEO

Transcriptome profiling (RNA-seq) of wild type and MYOCD overexpression in human lung cancer cell line A549.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) of wild type and MYOCD overexpression in human lung cancer cell line A549. Methods: mRNA profiles of wild type（WT） and MYOCD overexpression (MYOCD) human lung cancer cell line A549 were generated by deep sequencing, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR.

2019-03-30 | GSE128919 | GEO

Gene expression analysis in fly ovaries from wuho mutant

Project description:Purpose: The goal of this study is to analyze genes affected by wuho mutation in Drosophila ovary Ovarian mRNA prolife of 7 day old control flies and flies bearing wuho mutation, in duplicate, using Illumina NextSeq 500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2020-01-03 | GSE142829 | GEO

Transcriptome of E18.5 CHD4-M195I mouse hearts

Project description:Purpose: The goal of this study is to compare the cardiac transcriptome profiling (RNA-seq) of WT and CHD4-M195I hearts at E18.5 to conclude genes affected by this CHD4 mutation. Methods: mRNA profiles of E18.5 WT and CHD4-M195I mouse hearts were generated by deep sequencing, n=4 for each genotype, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: RNA-sequencing (RNA-seq) analyses on E18.5 WT and CHD4-M195I hearts and identified 323 genes that were differentially expressed [adjusted P value <0.05, |log2(Fold Change)| > 0.5], 113 upregulated and 210 downregulated in CHD4-M195I hearts.

2023-05-08 | GSE229050 | 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