Transcriptomic profile of hypodermal adventitia fibroblasts from Csf1f/f and Tek-crexCsf1f/f mice
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE228443 | GEO | 2023/09/06
REPOSITORIES: GEO
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Project description:To investigate the contributions of hypodermal ribosome biogenesis to organism-wide growth, we established C.elegans strains where RPOA-2 can be depleted globally or particularly in hypodermis using auxin-inducible degradation (AID) system. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different strains at 2 time points.
2022-11-29 | GSE213367 | GEO
Project description:The roundworm Caenorhabditis elegans is a heme auxotroph that requires the coordinated actions of HRG-1 heme permeases to transport environmental heme into the intestine and HRG-3, a secreted protein, to deliver intestinal heme to other tissues including the embryo. Here we show that heme homeostasis in the extraintestinal hypodermal tissue is facilitated by the transmembrane protein HRG-2. Systemic heme deficiency upregulates hrg-2 mRNA expression over 200-fold in the main body hypodermal syncytium hyp 7. HRG-2 is a type I membrane protein which binds heme and localizes to the endoplasmic reticulum and apical plasma membrane. Cytochrome heme profiles are aberrant in HRG-2 deficient worms, a phenotype that is partially suppressed by heme supplementation. Heme-deficient yeast strain, ectopically expressing worm HRG-2, reveal significantly improved growth at submicromolar concentrations of exogenous heme. Taken together, our results implicate HRG-2 as a facilitator of heme utilization in the C. elegans hypodermis and provide a mechanism for regulation of heme homeostasis in an extraintestinal tissue. Two experimental groups: Group 1: three 4um Controls vs. three 4uM hrg-2 Mutants; Group 2: three 20um Controls vs. three 20uM hrg-2 Mutants
2013-01-01 | E-GEOD-34471 | biostudies-arrayexpress
Project description:To explore the effect of cell-autonomous Igf1 expression on hypodermal macrophages, these cells were isolated from Csf1r-cre x Igf1-flox mice and subjected to single-cell ATAC-sequencing.
2023-09-06 | GSE227859 | GEO
Project description:The roundworm Caenorhabditis elegans is a heme auxotroph that requires the coordinated actions of HRG-1 heme permeases to transport environmental heme into the intestine and HRG-3, a secreted protein, to deliver intestinal heme to other tissues including the embryo. Here we show that heme homeostasis in the extraintestinal hypodermal tissue is facilitated by the transmembrane protein HRG-2. Systemic heme deficiency upregulates hrg-2 mRNA expression over 200-fold in the main body hypodermal syncytium hyp 7. HRG-2 is a type I membrane protein which binds heme and localizes to the endoplasmic reticulum and apical plasma membrane. Cytochrome heme profiles are aberrant in HRG-2 deficient worms, a phenotype that is partially suppressed by heme supplementation. Heme-deficient yeast strain, ectopically expressing worm HRG-2, reveal significantly improved growth at submicromolar concentrations of exogenous heme. Taken together, our results implicate HRG-2 as a facilitator of heme utilization in the C. elegans hypodermis and provide a mechanism for regulation of heme homeostasis in an extraintestinal tissue.
2013-01-01 | GSE34471 | GEO
Project description:In order to explore and compare the transcriptomic profile of CCR2+ macrophages, CCR2- macrophages and dendritic cells present in the dermis and hypodermis of C57BL/6 mice, isolated cells were subjected to RNA-sequencing analysis.
2023-09-06 | GSE227758 | GEO
Project description:modENCODE_submission_662 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: DM8001 (engineered, target gene dpy-7 tagged by GFP); Tissue: hypodermis; Developmental Stage: Mixed stage of embryos 20dC; Genotype: raIs/[rol-6(SU1006)+Pdpy-7::GFP]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain DM8001 (engineered, target gene dpy-7 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue hypodermis
2010-08-04 | E-GEOD-23286 | biostudies-arrayexpress
Project description:To check the gene signatures of SEMA7A high and SEMA7Anegative IPF lung fibroblasts and the similarity of SEMA7A high fibroblasts and invasive fibroblasts, SEMA7A negative fibroblasts and noninvasive fibroblasts, we sorted the SEMA7A high and negative IPF lung fibroblasts by flow cytometry and performed total RNA-seq.
2019-12-31 | GSE137025 | GEO
Project description:The goal of these studies was to delineate mechanisms of crosstalk between the atherosclerotic arterial wall of the aorta and the peripheral nervous system (PNS) in aged hyperlipidemic ApoE-deficient mice. We had observed by immunohistochemistry and morphometry that axon density of the PNS in adventitia segments that were located adjacent to advanced atherosclerotic plaques of aged hyperlipidemic ApoE-deficient mice were markedly higher than those adventitia segments that did not show adjacent atherosclerotic plaques in the intima layer. It is noteworthy in this connection that neither the media nor the intimal layer are innervated by axon endings. However, the adventitia layer of arteries is a conduit for axons and nerves of the PNS connecting the peripheral ganglia and peripheral organs including the spleen. In addition, we discovered (see references below) that atherosclerosis is sensed by the immune system of aged ApoE-deficient mice resulting in the formation of artery tertiary lymphoid organs in the adventitia layer of the arterial wall. To examine potential molecular mechanisms of the crosstalk between the disease aorta and the PNS, we isolated adventitia tissues and media tissues from aortas of ApoE-deficient mice and used wild-type mice as controls. Moreover, we observed that the sympathetic nervous system paraaortic and periaortic ganglia in aged ApoE-deficient but not of aged wild-type mice were infiltrated by leukocytes indicating that atherosclerosis is associated with major alterations of the PNS including axonogenesis and ganglionitis. To identify potential molecules involved in the crosstalk, we isolated respective tissues (media, adventitia, ganglia) by laser capture microdissection and generated large scale mRNA expression arrays to construct transcript maps that were assembled into transcript atlases. Publications related to this approach: Artery Tertiary Lymphoid Organs Control Aorta Immunity and Protect against Atherosclerosis via Vascular Smooth Muscle Cell Lymphotoxin β Receptors. Hu D, Mohanta SK, Yin C, Peng L, Ma Z, Srikakulapu P, Grassia G, MacRitchie N, Dever G, Gordon P, Burton FL, Ialenti A, Sabir SR, McInnes IB, Brewer JM, Garside P, Weber C, Lehmann T, Teupser D, Habenicht L, Beer M, Grabner R, Maffia P, Weih F, Habenicht AJ. Immunity. 2015 Jun 16;42(6):1100-15. doi: 10.1016/j.immuni.2015.05.015. Artery tertiary lymphoid organs contribute to innate and adaptive immune responses in advanced mouse atherosclerosis. Mohanta SK, Yin C, Peng L, Srikakulapu P, Bontha V, Hu D, Weih F, Weber C, Gerdes N, Habenicht AJ. Circ Res. 2014 May 23;114(11):1772-87. doi: 10.1161/CIRCRESAHA.114.301137. Review. Control of dichotomic innate and adaptive immune responses by artery tertiary lymphoid organs in atherosclerosis. Weih F, Gräbner R, Hu D, Beer M, Habenicht AJ. Front Physiol. 2012 Jul 6;3:226. doi: 10.3389/fphys.2012.00226. Laser-capture microdissection of hyperlipidemic/ApoE⁻/⁻ mouse aorta atherosclerosis. Beer M, Doepping S, Hildner M, Weber G, Grabner R, Hu D, Mohanta SK, Srikakulapu P, Weih F, Habenicht AJ. Methods Mol Biol. 2011;755:417-28. doi: 10.1007/978-1-61779-163-5_35. apoE-Adventitia arrays were submitted previously (GSM252007, GSM252008, GSM252009, GSM252010, GSM252011, GSM252014, GSM252015, GSM252016; GSE10000, GSE40156) and are now submitted together with new wild-type adventitia arrays not previously published in order to make all adventitia of ApoE-deficient mice and wild-type mice available in one new submission/location.
2022-02-27 | GSE94044 | GEO
Project description:To adapt RNA polymerase DamID (RAPID) for FLP-mediated spatial control in Caenorhabditis elegans, we inserted a Dam::rpb-6 fusion gene downstream of a FRT-flanked mCh::his-58 cassette and under control of the hsp-16.41 promoter. We introduced a single copy of this construct into the C. elegans genome and crossed the resulting line with a dpy-7p::FLP driver to enable basal Dam::rpb-6 expression in the hypodermis. Nematodes were cultured at 20 degrees Celcius to ensure low levels of Dam::RPB-6 expression in the hypodermis and total genomic DNA was purified from L4 larvae. DNA from animals expressing GFP::Dam was used to control for unspecific methylation. The genome-wide association profile of Dam::RPB-6 was determined by deep sequencing, which revealed a list of 2331 protein coding genes with FDR < 0.05. Original RAPID reference: Gomez-Saldivar et al (2020) Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Genetics 216, 931–945. doi:10.1534/genetics.120.303774
2022-09-30 | GSE214300 | GEO
Project description:To adapt SLAM-ITseq for Caenorhabditis elegans, we inserted a codon-optimized version of the Toxoplasma gondii UPRT gene downstream of a FRT-flanked mCh::his-58 cassette and under control of the strong and ubiquitous eft-3 promoter. We introduced a single copy of this construct into the C. elegans genome and crossed the resulting line with a dpy-7p::FLP driver. FLP-dependent expression of UPRT was confirmed by Western blotting (strain BN1190). As a proof of concept, we exposed animals to 4-TU from L3 to L4 stage and purified total RNA. RNA from animals without FLP expression was used to control for UPRT-independent labeling strain BN1158). RNA was alkylated with iodoacetamide, which leads to a T>C conversion of 4-TU-labeled positions during cDNA synthesis, and subjected to deep sequencing (see Materials and Methods). We confirmed that the presence of FLP and UPRT did not affect gene expression. Comparing the T>C conversion rate per gene revealed a significant increase in nematodes expressing UPRT in the hypodermis. Next, we performed a beta-binominal test to identify genes that were significantly labelled across all replicas, which retrieved 197 genes (p<0.003; FDR<0.1 after adjustment for multiple comparisons). Original SLAM-ITseq reference: Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA (2018) SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting. Development 145 (13). doi:10.1242/dev.164640
2022-12-31 | GSE192419 | GEO