Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' Transcriptomes in lymphoma

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' Transcriptomes in lymphoma

PROVIDER: PRJNA481246 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7524660_1.fastq.gz	Fastqsanger.gz
	SRR7524660_2.fastq.gz	Fastqsanger.gz
	SRR7524661_1.fastq.gz	Fastqsanger.gz
	SRR7524661_2.fastq.gz	Fastqsanger.gz
	SRR7524656_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' Transcriptomes in lymphoma

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in Ctrl-Cas9 and TRIB3-Cas9 lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: Ctrl-Cas9 and TRIB3-Cas9 cells' mRNA profiles 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 following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2020-10-01 | GSE117128 | GEO

Genome-wide maps of chromatin state in TRIB3-shRNA and control lymphoma cells

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of RNAPII with promoters in mammalian cells. We performed ChIP sequencing with antibody to total RNAPII in TRIB3-cas9 and control group. Inspection of multiple individual traces and global analyses showed that TRIB3 deletion globally reduced association of RNAPII with promoters.

2020-10-02 | GSE126743 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of WT and GSH or Ctrl and Cas9 mouse breast cancer cells Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in WT and WT+GSH or Ctrl-Cas9 and Scarb2-Cas9 mouse breast cancer cells by using NGS-derived transcriptome profiling (RNA-seq). Methods: 4T1 cells treated with or without GSH (500 µM) and 4T1 stably expressing Ctrl-Cas9 or Scarb2-Cas9 were collected. These cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of WT and WT+GSH or Ctrl-Cas9 and Scarb2-Cas9 mouse breast cancer cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2024-10-09 | GSE252087 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in Ctrl-siRNA and c-Myc-siRNA lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: Ctrl-siRNA and c-Myc-siRNA cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of Ctrl-siRNA and c-Myc-siRNA cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2020-10-02 | GSE126739 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

| PRJNA523180 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of EL4+Ctrl and EL4+RGFP966 cells' Transcriptomes in T cells lymphoma

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of EL4+Ctrl and EL4+RGFP966 cells' Transcriptomes in T cells lymphoma

| PRJNA1017862 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of WT and GSH or Ctrl and Cas9 mouse breast cancer cells Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of WT and GSH or Ctrl and Cas9 mouse breast cancer cells Transcriptomes

| PRJNA1057739 | ENA

The effect of TRIB3 overexpression on mouse hepatocytes

Project description:To investigate the effect of TRIB3 overexpression on regulation of lipid metabolism in hepatocytes, we isolated mouse primary hepatocytes from AAV-GFP or AAV-Trib3 mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of two groups of mouse primary hepatocytes from AAV-GFP or AAV-Trib3 mice.

2023-05-28 | GSE232807 | GEO

Genome-wide maps of chromatin state in TRIB3-shRNA and control lymphoma cells

Project description:Genome-wide maps of chromatin state in TRIB3-shRNA and control lymphoma cells

| PRJNA523177 | ENA

mRNA expression of Control or TRIB3-silenced MCF7 cells

Project description:Investigation of whole genome gene expression level changes in TRIB3-silenced MCF7 cells as compared to Control MCF7 cells. Analysis of activity changes of pathways for FOXO1 phosphorylation between TRIB3-silenced and Control MCF7 cells.

2019-09-25 | GSE116671 | 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