Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential impact of LPS and LTA stimulation on differentiated bone marrow and Yolk sac Hoxb8 macrophages

ABSTRACT: The impact of LPS and LTA stimulation on differentiated bone marrow and Yolk sac Hoxb8 macrophages in comparison to untreated control cells was studied by global protein profiling using a bottom-up approach.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Early Embryonic Cell, Macrophage

DISEASE(S): Disease Free

SUBMITTER: Elke Hammer

LAB HEAD: Elke Hammer

PROVIDER: PXD026922 | Pride | 2022-02-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	170728_OV4_JP__BM_2_1_star.raw	Raw
	170728_OV4_JP__BM_2_2_star.raw	Raw
	170728_OV4_JP__BM_2_3_star.raw	Raw
	170728_OV4_JP__BM_2_4_star.raw	Raw
	170728_OV4_JP__LPS_BM_1.raw	Raw

Items per page:

1 - 5 of 28

Similar Datasets

Expression data from Tnrc6a (GW182) mutant yolk sac

2011-09-01 | GSE30244 | GEO

Expression data from Tnrc6a (GW182) mutant yolk sac

Project description:GW182 (Tnrc6a) is a key component of RISC (miRNA-Induced Silencing Complex) that plays a critical role in miRNA-mediated gene silencing. Here, we show that GW182 is expressed in the yolk sac endoderm, and that gene-trap disruption of GW182 leads to growth arrest of yolk sac endoderm, impaired hematopoiesis and embryonic lethality. To investigate roles of GW182 in the yolk sac endoderm, we assessed changes in mRNA expression in the yolk sac of E9.5 GW182gt/gt embryos using microarrays (Affymetrix). Yolk sac of wild type littermates and GW182gt/gt embryos at E9.5 was collected for total RNA isolation using Trizol (Invitrogen). RNAs were purified according to the manufacturer’s protocol before subjected to Mouse Gene 1.0 ST Whole Genome Array (Affymetrix) for mRNA expression profiling. Experiments were performed in triplicate. Differentially expressed mRNAs were identified using a two-sample t-test (P<0.05 considered significant).

2011-08-31 | E-GEOD-30244 | biostudies-arrayexpress

Human fetal yolk sac scRNA-seq data (sample ID: F158 for Haniffa Lab; 16099 for HDBR)

Project description:Investigating the blood, immune and stromal cells present in a human fetal embryo in a world first single cell transcriptomic atlas. The embryo was dissected into 12 coronal sections, yolk sac, and yolk sac stalk. Live single cells sorted, with cell suspension then undergoing 10x chromium 5 prime scRNA-seq. This accession contains the yolk sac and yolk sac stalk data from this embryo. A matched accession contains the coronal section data. Lane "WS_wEMB12142156" (from yolk sac) was excluded from downstream analysis due to low fraction reads in cells post-CellRanger QC. Termination procedure for this embryo was medical. The F158_[features...barcodes...matrix].[tsv...mtx].gz files attached to this accession represent raw count data from all the 10x lanes in this accession combined, and as output from CellRanger filtered matrices (CellRanger version 6.0.1 using human reference genome GRCh38-2020-A). One set of count matrices relates to the yolk sac data, and one set of count matrices relates to the yolk sac stalk data.

2022-12-07 | E-MTAB-11673 | biostudies-arrayexpress

The role of the yolk sac in human fetal development and identification of a hepatocyte-like cell in the human yolk sac

Project description:The human yolk sac (YS) is an extra-embryonic tissue critical for early prenatal life development. It is the first site of haematopoiesis where progenitors differentiate from endoderm within blood islands of the yolk sac contributing initially to primitive erythropoiesis and in subsequent waves to erythro-myeloid and lymphoid differentiation.

2023-03-01 | E-MTAB-10552 | biostudies-arrayexpress

The role of the yolk sac in human fetal development and identification of a hepatocyte-like cell in the human yolk sac (SS2)

2023-03-01 | E-MTAB-10888 | biostudies-arrayexpress

RNA sequencing of Hoxb8 yolk sac- and bone marrow-derived

Project description:Progenitor cells of yolk sac and bone marrow origin were transduced with an estrogen receptor Hoxb8 fusion protein to generate stable cell lines. Macrophages were differentiated with M-CSF in the absence of estrogen, and then stimulated with IL-4 or LPS. Hoxb8 progenitor cells and differentiated macrophages were analyzed by RNA sequencing.

2022-01-10 | GSE176409 | GEO

Self-organized yolk sac-like organoids allow for scalable generation of multipotent hematopoietic progenitor cells from human induced pluripotent stem cells

Project description:The human definitive yolk sac is an important organ supporting the early developing embryo through nutrient supply and by facilitating the establishment of the embryonic circulatory system. However, the molecular and cellular biology of the human yolk sac remains largely obscure due to the lack of suitable in vitro models. Here, we show that human induced pluripotent stem cells (hiPSCs) co-cultured with various types of stromal cells as spheroids self-organize into yolk sac-like organoids without the addition of exogenous factors. Yolk sac-like organoids recapitulated a yolk sac specific cellular complement and structures as well as the functional ability to generate definitive hematopoietic progenitor cells (HPCs). Furthermore, sequential hemato-vascular ontogenesis could be observed during organoid formation. Notably, our organoid system can be performed in a scalable, autologous, and xeno-free condition, thereby providing an important model of human definitive yolk sac development and allows for efficient bulk generation of hiPSC-derived HPCs.

2021-05-05 | GSE157140 | GEO

Comparison of gene expression pattern between Wild-type and Hypb knockout embryo yolk sacs

Project description:This study aimed at exploring the physiological function of mammalian HYPB by means of knockout mouse model. Homogenous disruption of mouse Hypb gene leads to embryonic lethality at E10.5-E11.5. Severe vascular defects were observed in the Hypb-/- embryos, yolk sac and placenta.In the mutant embryo and yolk sac, disorganized and abnormally dilated capillaries cannot be remodeled into large blood vessels or intricate networks. Thus, our results suggest that the mammalian HYPB HMT plays an important role in embryonic vascularization. Keywords: knockout, mouse embryo development, angiogenesis, yolk sac, E9.0, E10.5

2009-12-28 | GSE10113 | GEO

Gene expression profiling of rudhira null embryo and yolk sac at 9.5 dpc

Project description:Rudhira is essential for mouse developmental angiogenesis and tissue morphogenesis. Embryos lacking endothelial rudhira die at mid-gestation with vascular patterning defects. Rudhira mutant yolk sac endothelial cells show slow and random migration. So to identify key signaling pathways perturbed in the absence of rudhira, we undertook whole transcriptome based analysis of gene expression in rudhira null yolk sac and embryo. Transcriptome analysis shows that key mediators of angiogenesis, cell adhesion, migration and extracellular matrix degradation as well as several components of the TGFÎ² pathway are perturbed in rudhira null mutant yolk sacs at 9.5 dpc. We used two embryo samples ( 2E- wild type; 5E- rudhira mutant). Repetition was done on each sample. We used 4 yolk sac samples (3Y,4Y- wild type; 7Y,8Y-rudhira mutant) for the analysis. Repetition was done on each sample.

2015-12-31 | E-GEOD-69204 | biostudies-arrayexpress

Comparative genomic analysis of basal and LPS-induced expression patterns of bone marrow derived macrophages and bone marrow resident macrophages

Project description:Comparative genomic analysis of basal and LPS-induced expression patterns of bone marrow derived macrophages and bone marrow resident macrophages demonstrates completely divergent transcriptome profile and indicates/confirms the existance of two distinct monocyte/macrophage populations in murine bone marrow. Most resident tissue macrophages descent from embryonic precursors of the yolk sac but inflammatory and bone marrow (BM) macrophages are considered to develop from hematopoietic stem cells (HSCs) in the BM. We now identified a novel subpopulation of resident CD163+ macrophages in the BM which were phenotypically and functionally distinct from classical BM-derived macrophages. Bioinformatics analysis of transcriptoms indicated a unique immune-modulatory phenotype of CD163+ macrophages. Cell fate studies in Csf1rMer-iCre-Mer;RosaLSL-GFP mice demonstrated that resident CD163+ macrophages of the BM do not develop from HSCs but descent from embryonic progenitors in the yolk sac strictly dependent on transcription factor IRF8. In contrast to other yolk sac derived tissue macrophages CD163+ cells seem to play a relevant role in infections and sterile inflammation. IRF8-/- mice lacking this population are highly sensible to S. aureus infections. Thus, CD163 defines a macrophage population resident in the bone marrow but originating from yolk sac progenitors which exhibits immune-modulatory properties under different inflammatory conditions. We used quantitative RNA-seq to perform whole transcriptome analysis and compare the transcriptomes of resident CD163+ BM macrophages and classical CD163- BMDM in steady state and after LPS stimulation.

2017-01-31 | GSE92618 | 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