Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-sequencing of QKI proficient and deficient microglia

ABSTRACT: RNA-sequencing of QKI proficient and deficient microglia

PROVIDER: PRJNA656802 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12439813_1.fastq.gz	Fastqsanger.gz
	SRR12439813_2.fastq.gz	Fastqsanger.gz
	SRR12439814_1.fastq.gz	Fastqsanger.gz
	SRR12439814_2.fastq.gz	Fastqsanger.gz
	SRR12439815_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

RNA-sequencing of QKI proficient and deficient microglia

Project description:Purpose:RNA_sequencing analysis defined a novel role for the QKI in microglia Methods: microglia mRNA profiles of 4-6 weeks-old wild-type (QKIfl/fl) and microglia specific knockout (QKIfl/fl; cx3r1cre-ert2) mice were generated by Illumina HiSeq 4000 in triplicate. The sequence reads that passed quality filters were trimmed with Trimmomatic v0.39. STAR v2.7.1a was then used to align the reads to the mouse genome (mm10/GRCm38). Gene expression was quantified across all samples with HOMER v4.11.1, and the normalization was carried out through the regularized logarithm (rlog) transformation of DESeq2 v1.26.0. Differential expression between the WT and knockout samples were calculated through DESeq2 v1.26.0, and the gene expression was considered significantly different if the absolute value of the log-fold-change (LFC) was higher than 2, the base means larger than 10 and the false discovery rate (FDR) less than 0.05. Results: RNA-seq data revealed the up-regulation of 326 genes and down-regulation of 294 genes in knockout microglia compare to wt (2-fold change at FDR of 0.05, base mean>10). In particular qkICx3cr1-KO microglia exhibited higher expression of genes that are known to encode proteins related to inflammation (Il-6, Apoe, Cxcl-10, Il-1b, Il-12b, and Tnf). In line with this, functional annotation by DAVID, Reactome and, GO analysis showed enrichment of cell cycle and inflammation-related pathways in the up-regulated transcripts in qkICx3cr1-KO mice. Up-regulated transcripts were further validated using qRT-PCR. Conclusions: Our study represents the first detailed analysis of microglia transcriptomes without QKI expression, with biologic replicates, generated by RNA-seq technology. The data should provide how QKI modulates the microglia gene expression profiles in genome-wide detail.

2020-10-30 | GSE156118 | GEO

RNA-sequencing of PRMT1 proficient and deficient microglia

Project description:RNA-sequencing of PRMT1 proficient and deficient microglia

| PRJNA828567 | ENA

ChIP-sequencing of PRMT1 proficient and deficient microglia

Project description:ChIP-sequencing of PRMT1 proficient and deficient microglia

| PRJNA844360 | ENA

RNA-sequencing of PRMT1 proficient and deficient microglia

Project description:RNA_sequencing analysis defined a novel role for the PRMT1 in microglia during normal and 0.2% cuprizone diet 5weeks We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

2022-04-29 | GSE201145 | GEO

ChIP-sequencing of PRMT1 proficient and deficient microglia

Project description:ChIP_sequencing analysis defined a novel role for the PRMT1 in microglia during normal and 0.2% cuprizone diet 5weeks We then performed ChIP analysis using data obtained from ChIP-seq of microglia at two time points

2022-06-14 | GSE205309 | GEO

Transcriptomic profile of cohesin proficient and deficient cells

Project description:Transcriptomic profile of cohesin proficient and deficient cells

| PRJNA515514 | ENA

Transcription profiling of mouse CD3e-proficient and deficient thymoma cells

Project description:Gene expression profiles of CD3e-proficient and CD3e-deficient were analysed using Affymetrix cDNA arrays (MOAE430)

2009-03-03 | E-MEXP-1590 | biostudies-arrayexpress

RNA-seq of RBM42-proficient and -deficient HCT116 cell line after VP16 treatment

Project description:To explore the role of RBM42 in the DNA damage response, we sought to determine the transcriptome of RBM42-proficient and -deficient cells following DNA damage induction. RNA samples were prepared from etoposide (VP16) treated HCT116 cells transfected with control or RBM42 siRNA, and subjected RNA-seq.

2022-12-15 | E-MTAB-11877 | biostudies-arrayexpress

Genome-wide gene expression analysis in ARID1A-proficient and ARID1A-deficient cancer cells

Project description:To investigate that ARID1A regulates transcription of genes encoding components of the GSH synthesis pathway, a genome-wide expression analysis of a panel of ARID1A-proficient and ARID1A-deficient cancer cells was performed.

2019-01-28 | GSE122926 | GEO

Comparison of tenascin-C proficient versus tenascin-C deficient Mouse Embryonic Fibroblasts (MEFs)

Project description:In order to investigate what signalling pathways are turned on by tenascin-C, we generated Mouse Embryonic Fibroblasts (MEFs) deficient for tenascin-C and compared their gene expression profile to MEFs proficient for tenascin-C.

2011-02-22 | GSE23547 | 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