Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

5 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of Zbtb10 Knockdown and Control cDC1 dendritic cells (Cd8+)

ABSTRACT: RNA-seq of the immune-suppressed cDC1 was done to look into the mechanism underlying TLR9. It was then compared with the inflammatory cDC1 DCs.

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Mus musculus

SUBMITTER: Sunil Raghav

PROVIDER: E-MTAB-9495 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq from ZEB1 Knockdown and Control CD8+cDC1

Project description:To have a mechanistic insight how the Zeb1 KD CD8+cDC1 perturbs the immune response globally. to identify the genes that are regulated by Zeb1 RNA was isolated and check for quality, then we used NEB RNA library preparation kit to prepare the library and send for sequencing on Illumina Hi-seq 2500 platform

2018-11-13 | E-MTAB-6916 | biostudies-arrayexpress

RNA-seq of Control and SMRT KD CD8α+ DCs at 0hr and 6hr CpG stimulation

Project description:RNAseq was performed to understand the role of SMRT in CD8α+ DCs. MutuDC cell line was transduced with empty and smrt shrna lentiviral particles and cells were prepared in unstimulated or 6hr CpG stimulation condition.

2022-09-20 | E-MTAB-10864 | biostudies-arrayexpress

RNA-seq of Control and SMRT KD CD8α+ DCs at 0hr and 6hr CpG stimulation

Project description:RNAseq were performed to understand the role of SMRT in CD8α+ DCs. MutuDC line were transduced with empty vector and SMRT shRNA using lentivirus and cells were prepared in unstimulated or 6hr CpG stimulation condition.

2022-09-20 | E-MTAB-10070 | biostudies-arrayexpress

CMTM6 drives cisplatin resistance by regulating AKT mediated Wnt signaling

Project description:The RNA-seq library preparation was performed for H357 CisR Nt Sh and H357 CisR CMTM6 shRNA treated with vehicle control (UT) and cisplatin (10 μM) (CisT) for 24 h. We have included two independent biological replicates to identify the CMTM6 downregulation mediated global transcriptome changes. For RNA-seq library preparation 2 μg of total RNA was used to isolate mRNA through magnetic beads using mRNA isolation kit (PolyA mRNA isolation Module, NEB) followed by RNA-seq library preparation using mRNA library preparation kit (NEB) strictly following the vendor recommended protocol. After library preparation concentration of libraries was estimated using qubit 2.0 (Invitrogen) and the recommended fragmentation sizes were confirmed by Tapestation (Agilent).

2021-02-08 | E-MTAB-9424 | biostudies-arrayexpress

RRBP1 rewires Cisplatin resistance in Oral Squamous Cell Carcinoma by regulating YAP-1

Project description:The RNA-seq library preparation was performed on H357 CisS at 0 month,H357 CisR at 4 months, and H357 CisR at 8 months whereas CisR represent Cisplatin drug resistance and CisS denote sensitive to Cisplatin. Additional, we also performed gene specific knockdown on H357CisR 8 months RRPB1 Sh. In experiment, We have added two independent biological replicates of each samples to understand the role of causative factor for cisplatin resistance at transcriptomic level. Total RNA isolated from above mentions experiment and 2 μg of RNA was used to prepared library. The mRNA was isolated through magnetic beads using mRNA isolation kit (PolyA mRNA isolation Module, NEB) followed by RNA-seq library preparation using mRNA library preparation kit (NEB) strictly following the vendor recommended protocol. After library preparation concentration of libraries was estimated using qubit 2.0 (Invitrogen) and the recommended fragmentation sizes were confirmed by Tapestation (Agilent).

2020-12-31 | E-MTAB-9697 | biostudies-arrayexpress

ZEB1 ChIP-seq Data from Control CD8+cDC1

Project description:To identify the direct targets of Zeb1 we performed ChIP-seq of wild type cDC1 cell line in unstimulated condition. cDC1 cell line was used for Chromatin Immunoprecipitation, it was then fixed and crosslinked and then fragmented and the fragmented DNA-protein was immunoprecipated using Zeb1 antibody. The chromatin sample was then used to prepare library using NEB kit following the manufacturer's protocol

2018-11-13 | E-MTAB-6917 | biostudies-arrayexpress

Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.

2019-11-12 | PXD010845 | Pride

Nuclear Receptor Co-repressor NCoR1 governs immune-tolerance in conventional dendritic cells by fine-tuning glycolysis and fatty acid oxidation

Project description:In this study, we focused on demonstrating the metabolic aspect of NCoR1 in the regulation of dendritic cells (DCs) functionality. We report that NCoR1 deficient tolerogenic DCs meet their anabolic requirements through enhanced glycolysis and OxPhos, supported by FAO-driven oxygen consumption. Furthermore, individual and dual inhibition of glycolysis through HIF-1α inhibitor (KC7F2) and fatty acid oxidation through CPT1 inhibitor (etomoxir) significantly impaired the secretion of tolerogenic cytokines. To validate the same at the global mRNA level we did bulk RNA-seq to determine the differentially expressed genes in control and NCoR1 KD 6h CpG activated DCs with and without inhibitor treatment.

2024-01-01 | E-MTAB-12066 | biostudies-arrayexpress

RNA-seq of Control and NCoR1 KD CD8α+ DCs at 0hr and 6hr of stimulation

Project description:RNA-seq was performed to understand the role of NCoR1 in CD8α+ DCs. MutuDC cell line was transduced with empty and Ncor1 shrna lentiviral particles and cells were prepared in unstimulated, 2hr and 6hr (IFNg, pIC and CpG+pIC+IFNg) stimulation condition.

2022-09-20 | E-MTAB-10989 | biostudies-arrayexpress

RNA sequencing of primary isolated unstimulated murine splenic DC1 and DC2 from specific pathogen free (SPF), Germ free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice

Project description:The transcriptomes of primary isolated unstimulated murine splenic cDC1 and cDC2 from specific pathogen free (SPF) were compared to cDC1 and cDC2 from Germ Free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice. Total RNA was prepared from sort-purified cDC1 and cDC2 (for each sample 3 individual mice were pooled) using Trizol reagent (Invitrogen) in combination with the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. For poly-A-dependent cDNA synthesis and a first amplification step 10 ng of total RNA was used as input in the Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) and processed according to the manufacturer’s instructions. 1 ng of the purified cDNA was used for tagmentation and library completion with the Nextera XT library preparation kit (Illumina). In the following, 2x75nt paired-end sequencing was performed on a NextSeq 500.

2020-03-30 | E-MTAB-8883 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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