Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiomic Profiling Reveals Metabolic Alterations Mediating Aberrant Platelet Activity and Inflammation in Myeloproliferative Neoplasms [mouse RNA-Seq]

ABSTRACT: To study therapeutic impacts of α-KG on MPN, cKIT+ cells from JAK2 V617F CD45.2 C57BL/6J mice were isolated and transplanted into irradiated CD45.1 C57BL/6J mice. Two weeks after transplant, mice were randomly grouped and supplemented with regular water or 1% α-KG in drinking water daily for 6 weeks. Bone marrow samples were collected for bulk RNA-seq analysis.

ORGANISM(S): Mus musculus

PROVIDER: GSE244587 | GEO | 2024/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Dynamic DNA methylation reveals novel cis-regulatory elements in murine hematopoiesis

Project description:Genome wide DNA methylation profiling of 9 different cell types of the murine hematopoietic system. The samples comprise FACS-sorted biological triplicates of hematopoietic stem and progenitor cells (LSK, CMP, GMP, MEP) and terminally differentiated immune cells (monocytes, neutrophils, CD4+ T-cells, CD8+ T-cells, B-cells). Additionally, bone marrow of CD45.1 (B6.SJL-Ptprca Pepcb/BoyCrl) and CD45.2 (C57BL/6J) mice as well as JAK2-V617F mutant mice was analyzed. The Illumina Infinium Mouse Methylation BeadChip was used to generate DNA methylation profiles across approximately 285,000 CpGs in these samples.

2022-11-08 | GSE201923 | GEO

scRNA-seq analysis of mouse splenic CD8 T cells 1 month post transfer of CD8 T cells from 3 months old donor into 24 months old recipient

Project description:Aging is associated with systemic chronic inflammation (inflammaging) that leads to impaired physiological functions and vulnerability to several diseases. However, underlying alterations in aged immune system resulting in gradual loss of immune fitness remain unclear. Using a combination of CD8 T cell transfer from young to old and from old to young mice and single-cell RNA sequencing, we characterized the age-associated alterations in CD8 T cells. We transferred 2 millions of purified CD8+ T cells pooled from 3 CD45.1 C57BL/6J 3 months old female mice (donor) by i.v. injection into CD45.2 C57BL/6J 24 months old female mouse (recipient) and sorted CD45.1+CD3e+CD8a+ and CD45.2+CD3e+CD8a+ T cells from the spleen 1 month post transfer to perform scRNA/TCR-seq.

2020-12-06 | GSE155005 | GEO

Nanostring analysis of macrophage subsets following zymosan-induced peritonitis

Project description:Resident macrophages from naïve mice or resident/inflammatory macrophages from mice treated with zymosan(10ug) 3 days prior were purified from C57BL/6 CD45.2+ donor mice. Purified populations were transferred into mirroring CD45.1/2+ recipient mice or clodronate pre-treated recipient mice. Donor populations were purified 8 weeks following transfer for Nanostring analysis.

2021-01-28 | GSE165036 | GEO

Effect of doxycycline treatment on germ-free mice

Project description:To characterize the mitochondrial stress response induced by Doxycycline in vivo in liver and kidneys, we administered doxycycline (Dox) at 500 mg/kg/day (mpkd) in the drinking water to 9 weeks-old germ-free C57BL/6J mice for 16 days, hence eliminating the potential confounding impacts of Doxycycline on the microbiome.

2022-09-14 | GSE202754 | GEO

XX chromosome complement promotes, and w-3 fatty acid treatment prevents, adverse statin effects in mice

Project description:RNA-sequening of livers from male and female C57BL/6J mice fed either chow diet or chow diet + simvastatin (0.1g/kg body weight) for 4 weeks.

2024-02-01 | GSE184588 | GEO

Single-cell RNAseq (10x Genomics) analysis of mouse splenic CD4+ T cells in WT and ∆Foxp3 mice and in WT/∆Foxp3 bone marrow chimeras

Project description:Single-cell RNAseq (10x Genomics) analysis of mouse splenic CD4+ T cells in WT and ∆Foxp3 mice and in WT/∆Foxp3 bone marrow chimeras. Mouse CD4+T cells in 21-day-old male WT and ∆Foxp3 mice were isolated from spleen by flow cytometry as DAPI–TCRβ+CD4+ cells for 10x Genomics Single Cell 3′ Reagent Kit (V2 chemistry, one sample per channel). For bone marrow chimera experiment: 7 week-old CD45.2-recipient mice were irradiated with 1000 Rad, reconstituted with 4 million CD3-depleted bone marrow cells: 50% CD45.1 x Foxp3-IRES-GFP (WT, 21d-old male) and 50% Foxp3DeltaEGFPiCre/RFP x ROSA-YFP x CD45.1/2 (scurfy, 21d-old male). 10 weeks later, spleen were harvested and tagged using a different Hashtags fo each mouse. ∆Foxp3 CD4+ T cells were sorted as DAPI–TCRb+CD4+CD45.1+CD45.2+. WT CD4+ T cells were sorted as DAPI–TCRb+CD4+CD45.1+CD45.2–. Control WT DAPI–TCRb+CD4+GFP+ Treg cells and GFP- Tconvs cells were also tagged and sorted. Samples with different hastags were pooled before single cell encapsulation using 10x Genomics Single Cell 3′ Reagent Kit (V3 chemistry).

2021-02-26 | GSE167575 | GEO

B cell-intrinsic STAT6 controls the germinal center response in type 2 immunity

Project description:By investigating the germinal center (GC) formation in STAT6ko/WT bone marrow-mixed chimera we found that GC formation in type 2 immune responses is dependent on B cell intrinsic expression of IL-4/IL-13-induced genes. We therefore used microarrays to find Stat6 dependent genes that are important for germinal center formation and/or organization after infection with the nematode Nippostrongylus brasiliensis (N. brasiliensis). Bone marrow of STAT6ko (CD45.2+) and WT (CD45.1+) were mixed and injected in lethaly irradiated WT (CD45.1+) mice. After 8 weeks, 5 Bone marrow-mixed chimera were infected with N. brasiliensis and draining lymph nodes were collected at day 14 after the infection and pooled. RNA was isolated from sort-purified CD45.1+ or CD45.2+ GC B cells (B220+CD38loGL-7hi).

2014-05-26 | E-GEOD-47679 | biostudies-arrayexpress

Capacity of yolk sac macrophages, fetal liver and adult monocytes to colonize an empty niche and develop into functional tissue resident macrophages

Project description:Tissue-resident macrophages can derive from yolk sac macrophages, fetal liver monocytes or adult bone marrow monocytes. Whether these precursors can give rise to transcriptionally identical alveolar macrophages is unknown. Here, we transferred traceable yolk sac macrophages, fetal liver monocytes, adult bone marrow monocytes or adult alveolar macrophages as a control, into the empty alveolar macrophage niche of neonatal Csf2rb-/- mice. All precursors efficiently colonized the alveolar niche and generated alveolar macrophages that were transcriptionally almost identical, with only 22 genes that could be linked to their origin. Underlining the physiological relevance of our findings, all transfer-derived alveolar macrophages self-maintained within the lungs for up to 1 year and durably prevented alveolar proteinosis. Thus, precursor origin does not affect the development of functional self-maintaining tissue-resident macrophages. CD45.1+CD45.2+ yolk sac macrophages, fetal liver monocytes, adult bone marrow monocytes or adult alveolar macrophages from the bronchoalveolar lavage were sorted from wild type CD45.1+CD45.2+ mice of indicated ages. From part of these samples RNA was isolated. The other part was transferred intranasally into the lungs of neonate Csf2rb-/- mice. 6 weeks post-transfer, transfer-derived CD45.1+CD45.2+ alveolar macrophages were sorted from the bronchoalveolar lavage. Wild type CD45.1+CD45.2 alveolar macrophages from the bronchoalveolar lavage of 6 week old mice were sorted as control. 36 samples (arrays) in total. RNA was isolated, amplified with Nugene pico kit, converted to cDNA and then hybridised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.

2016-03-01 | E-GEOD-76999 | biostudies-arrayexpress

Ileum Microarray Data from Transcriptomics Driven Lipidomics (TDL) identifies the microbiome-regulated targets of ileal lipid metabolism Study

Project description:Microbiome regulation of lipid metabolism Germfree male C57BL/6J mice were purchased at 8 weeks of age from Charles River Laboratories (L'Arbresle, France). Mice were treated with 10^8 CFU/mL E. coli M8 strain (isolated from the feces of an ob/ob mouse) in drinking water for 14 days. At the end of the treatment, mice were subjected to an oral lipid tolerance test (OLTT) (with 6ml/kg of corn oil) after overnight fasting (14h). All mice were sacrificed 6 hours after the lipid tolerance test and ileum samples were collected for further analysis.

2017-11-08 | GSE99018 | GEO

Gene expression changes induced by Dendrocalamus latiflorus leaf extract (DLE) and white tea extract (WTE) and pioglitazone (PGZ) in db/db mice liver

Project description:Eight-week-old C57BL/6J and T2DM db/db mice randomly divided into 4 groups of 8 based on equal bodyweight and fasting blood glucose (FBG) levels (mice were fasted for 6 h). The C57BL/6J mice (normal group) were treated with saline. The T2DM db/db mice were treated with saline, DLE (200 mg/kg), WTE (180 mg/kg), or pioglitazone (PGZ, 20 mg/kg) for 12 weeks, and were called the model group, DLE group, WTE group and PGZ group, respectively. All mice received oral administration of the indicated treatments once a day. After 12 weeks drug administration, liver aliquots from four randomly selected mice from the normal, model, PGZ and DLE groups were ground into powder in liquid nitrogen, followed by RNAseq for differentially expressed gene determination and pathway enrichment analysis.

2021-04-01 | GSE171269 | GEO

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