Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq in mouse Th17 cells

ABSTRACT: Purpose: To gain more mechanistic insights into the effects of LDHB deletion on T cells, we performed RNAseq in WT and LDHB cKO Th17 cells which cultured in 5% O2. Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA). RNA-seq libraries were generated using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA). Approximately 60–80 million paired-end 150 bp reads were generated per sample using Illumina HiSeq 4000 platform Results: RNA-seq revealed quite small different transcriptome patterns

ORGANISM(S): Mus musculus

PROVIDER: GSE190799 | GEO | 2023/03/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA seq in CD8T cells

Project description:Purpose: we evaluated the T cell mediated anti tumor immune response under asparagine restriction Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA). RNA-seq libraries were generated using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA). Approximately 60–80 million paired-end 150 bp reads were generated per sample using Illumina HiSeq 4000 platform Results: We performed gene expression profiling analysis using data obtained from RNA-seq of T cells cultured in presence and absence of asparagine at 3 different time points and found that asparagine restriction induces biphasic response in T cell.

2023-06-15 | GSE201870 | GEO

RNA-seq in mouse WT and ABAT cKO T cells

Project description:Purpose: To gain more mechanistic insights into the effects of ABAT deletion on T cells, we performed RNAseq in activated CD4 WT and ABAT cKO TH0 cells. Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA). RNA-seq libraries were generated using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA). Approximately 60–80 million paired-end 150 bp reads were generated per sample using Illumina HiSeq 4000 platform Results: RNA-seq revealed an decreased pro-inflammatory gene signature in ABAT cKO T cells after activation Conclusions: Inhibition of ABAT suppresses TH17 but enhances iTreg cell differentiation

2022-08-02 | GSE190818 | GEO

RNA seq of mouse CD4 T cells

Project description:Purpose: To gain more mechanistic insights into the effects of SDHB deletion on T cells, we performed RNAseq in activated WT and SDHB cKO T cells. Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA). RNA-seq libraries were generated using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA). Approximately 60–80 million paired-end 150 bp reads were generated per sample using Illumina HiSeq 4000 platform Results: RNA-seq revealed an enriched pro-inflammatory gene signature in SDHB cKO T cells after activation Conclusions: SDH inactivation results in a pro-inflammatory gene signature in T cells after activation

2022-03-08 | GSE184743 | GEO

Gene expression changes in cutting and inverted cutting in Populus yunnanensis at the primary and rapid growth stages respectively

Project description:Illumina technology was used to generate mRNA profiles of stem apex of Populus yunnanensis with cutting and inverted cutting. Total RNA was extracted separately from each plant and pooled to three biological replicates per condition. RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).

2023-12-08 | GSE249347 | GEO

Analysis of gene expression in Mel Z cells grown on plastic (MP).

Project description:RNA-Seq procedure was used for analysis of expression in melanoma cells. Cells were separately lysed with Trizol reagent (Invitrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 14.8 millions of reads were generated for each sample.

2024-10-08 | GSE221876 | GEO

RNA-Seq in HEK293T human cells

Project description:RNA-Seq procedure was used for analysis of expression in HEK293T cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 10 millions of reads were generated for each sample.

2019-12-03 | GSE130262 | GEO

Analysis of gene expression in Mel Z cells grown on Matrigel in the presence of inhibitor(MMI).

Project description:RNA-Seq procedure was used for analysis of expression in melanoma cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 14.8 millions of reads were generated for each sample.

2024-05-10 | GSE221873 | GEO

Analysis of gene expression in Mel Z cells grown on Matrigel (MM).

2024-05-10 | GSE221872 | GEO

RNA sequencing in human iPSCs derived from bipolar patients to identify important therapeutic molecular targets of Valproate(VPA)

Project description:Valproate(VPA) has been used in the treatment of bipolar disorder since the 1990s. However, the therapeutic targetsof VPA have remained elusive. Here we used RNA sequencing in human iPSCs derived from bipolar patients to further identify important molecular targets. Human iPSCs were homogenized and total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Hilden, Germany). RNA quantity and quality were assessed using fluorometry (Qubit RNA Broad Range Assay Kit and Fluorometer; Invitrogen, Carlsbad, CA) and chromatography (Bioanalyzer and RNA 6000 Nano Kit; Agilent, Santa Clara, CA), respectively. Libraries were prepared using TruSeq Stranded mRNA (PolyA+) kit (Illumina, San Diego, CA) and sequenced by Illumina NextSeq 500. The read length was 75bp with 30-40M reads per sample. FastQC (v0.11.3) was performed to assess data quality. TopHat2 (v2.0.9) aligned the reads to the mouse reference genome (Mus musculus UCSC mm10) and to the Ensembl human reference genome (GRCh38.p13) using default parameters. Alignments were then converted to expression count data using HTseq (v0.6.1) with default union mode.

2020-12-31 | GSE160761 | GEO

RNA seq of mouse CD3 T cells

Project description:Purpose: To gain more mechanistic insights into the effects of SDHB deletion in T cells, we performed RNAseq in activated WT and SDHB cKO T cells. Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA). Results: RNA-seq revealed an enriched pro-inflammatory gene signature in SDHB cKO T cells after activation Conclusions: SDH inactivation results in a pro-inflammatory gene signature in T cells after activation

2022-03-08 | GSE184010 | 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