Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tissue neutrophil heterogeneity

ABSTRACT: Purpose: The goals of this study are to compare bulk RNAseq profiles of tissue neutrophils. Methods: Bulk RNAseq of sorted neutrophils from bone marrow, spleen, blood, lung, peripheral blood, skin and intestine from wild-type (WT) mice, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the gene level with RSEM which mapped about 26 million sequence reads per sample to the mouse genome (build mm10/GRCm38) and identified 32328 genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE141745 | GEO | 2020/09/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Tissue neutrophil heterogeneity in germ free mice

Project description:Purpose: The goals of this study are to compare bulk RNAseq profiles of tissue neutrophils in germ free mice. Methods: Bulk RNAseq of sorted neutrophils from spleen, blood, lung from spf and germ free mice, using Illumina. The sequence reads that passed quality filters were analyzed at the gene level with RSEM.

2020-09-08 | GSE142432 | GEO

RNA-seq of tissue neutrophil

Project description:Purpose: Neutrophils in lung at steady states seems have different characteristics from blood neutrophils even both of them located intravascular regions. The goals of this study are to identify what make lung neutrophils different from other neutrophils from bone marrow and peripheral blood. Methods: Sorted CD11b+ Ly6G+ cells from bone marrow, blood, and lungs of C57BL/6 were investigated with RNAseq using Illumina. Results: Qualified sequence reads per sample to the mouse genome (mm10) with Bowtie2 or STAR were processed with StringTie and identified genes. Neutrophil mRNA profiles from bone marrow, blood and lung of 8 weeks old wild type C57BL/6. Conclusion : 2,032 genes were significantly different in lung neutrophils compared to blood neutrophils.

2022-08-01 | GSE199774 | GEO

RNA-seq of bone marrow neutrophil treated PGE2 or Vehicle

Project description:Purpose: Investigate the neutrophils could exspress different mRNA de novo from PGE2 stimulation. Methods: Isolated bone marrow neutrophils with Percoll gradient are treated with 10 μM of PGE2 for 24 hours. Results: Qualified sequence reads per sample to the mouse genome (mm10) with Bowtie2 or STAR were processed with StringTie and identified genes. Conclusion : 1,359 genes were significantly different in PGE2 treated bone marrow neutrophils from vehicle treated ones.

2022-08-01 | GSE199773 | GEO

Transcriptomic analysis of hippocampus of hACE2 mice with SARS-CoV-2 infection

Project description:The goals of this study are to dmonstrate transcriptomic profiling of SARS-CoV-2 infected brain samples. Hippocampal mRNA profiles of hACE2 transgenic mice at 30-day post SARS-CoV-2 infection were generated by bulk RNA sequencing, in 3 samples each group. Sequence reads were mapped to the mouse genome (GRCm38) using STAR. RSEM was used to count aligned reads that mapped to the annotated mouse genes. Gene-level differential expression analyses were performed using R package DESeq2. Results showed that SARS-CoV-2 infection led to long-term effect regarding neuroinflammation and neuronal function.

2022-09-30 | GSE199545 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and cardiac-specific Bmi1 deletion [mouse]

Project description:To explore the primary cause of Dilated Cardiomyopathy in Bmi1-null mice, we set out to identify differentially expressed genes by massively parallel sequencing of heart samples from Bmi1f/f;?MHCTM-Cretg/+ mice versus ?MHCTM-Cretg/+ control mice (17 weeks postinduction). Methods: Heart mRNA profiles of 17-weeks post-induction Bmi1f/f; MHCTM-Cretg/+ mice and MHCTM-Cretg/+ control mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. Sequence reads were pre-processed with Cutadapt 1.2.1, to remove TruSeq adapters and mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) using RSEM v1.2.3. The Bioconductor package EdgeR was used to normalize data with TMM and to test for differential expression of genes using GLM.

2015-01-13 | E-GEOD-64391 | biostudies-arrayexpress

Differential gene expression of neutrophils that lack lymphotoxin beta receptor identifies a metabolic gene signature

Project description:Isolating Neutrophils from mouse blood, we employed bulk RNAseq and DE gene expression analysis to determine pathways that are regulated downstream of LTBR in neutrophils.

2020-08-01 | GSE150243 | GEO

Sox2 suppresses gastric tumorigenesis in mice [RNA-seq]

Project description:Purpose: Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. The goal of this study is to determine the function of and the genes regulated by Sox2 in the stomach. Methods: mRNA profiles of Sox2 WT and Sox2 KO gastric glands were generated by RNA-sequencing, in triplicate, using a Illumina HiSeq 2500 instrument, resulting in 36 million single-end 50bp reads per smaple. Sequencing reads were mapped to the mouse reference genome (mm10/GRCm38) using STAR (Dobin et al., 2013). Read counts over transcripts were calculated using HTSeq v.0.6.0 (Anders et al., 2015) based on a current Ensembl annotation file for mm10/GRCm38 (release 75). Results: Sox2 is dispensiable for gastric stem cell self-renewal and epithelial homeostasis, however modulates the expression of cancer and intestinal related genes. mRNA profiles of stomachs from 10 week old Sox2 WT and Sox2 KO mice were generated by sequencing, in triplicate, using a Illumina HiSeq 2500.

2016-08-04 | E-GEOD-83964 | biostudies-arrayexpress

RNA-Seq transcriptome analysis of whole newborn lenses from FVB/N, Le-Cre and P0-3.9GFPCre mice

Project description:Here we report RNA-Seq data from RNA isolated from newborn lenses from FVB/N control mice as well as from newborn lenses of two different transgenic mouse lines (Le-Cre and P0-3.9GFPCre). Sequence reads of 51 bp were obtained from an illumine HiSeq 2000 system and mapped to the C57BL/6 reference genome (assembly GRCm38 (mm10)) using GSNAP software. Adapters and poor-quality regions were trimmed using Trimmomatic-0.36 software. Gene and isoform abundance was quantified using RSEM-1.3.0 software. Differential expression analysis was completed using DESeq2-1.10.1 software. For differential expression we used a cutoff value of equal to or greater than 1.5-fold change with an adjusted p value ≤ 0.05. The transcriptomes of both Le-Cre and P0-3.9GFPCre lenses closely matched the FVB/N control lenses. However, Le-Cre lenses exhibited deregulation of 15 murine genes, several of which are associated with apoptosis. In contrast, P0-3.9GFPCre lenses only deregulated two murine genes.

2019-02-26 | GSE125108 | GEO

miRNA overexpression modulates neutrophil migration

Project description:We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils, and RNAseq for identification of mRNA targets of miRNA-31, miRNA-190 and miRNA-375 in neutrophils

2022-02-25 | GSE167554 | GEO

Host transcriptome profile of children with respiratory virus infection

Project description:Purpose: The aim of this study is to determine the expression profile in whole blood samples of children infected with respiratory syncytial virus and other respiratory viruses. Method: Host mRNA profiles in whole blood samples of children were generated by next-generation sequencing using Illumina Hiseq. Sequence reads were trimmed for adapter using skewer, mapped to reference human genome using STAR, and quantified using RSEM. Differential expression analysis was performed using DESeq2. Results: Transcriptional module analysis revealed dysregulation of genes related to inflammatory response, neutrophils, monocytes, B-cell and T-cell response. Conclusion: This study showed an imbalance in innate and adaptive immune responses in children with respiratory virus infections. This study also showed that NGS provides a comprehensive assessment of transcripts in whole blood samples.

2021-01-29 | GSE155925 | 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