Primary male adult tail fibroblast cell-state specific response to proteasome inhibition
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA734920 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14718100_1.fastq.gz | Fastqsanger.gz | |||
| SRR14718100_2.fastq.gz | Fastqsanger.gz | |||
| SRR14718101_1.fastq.gz | Fastqsanger.gz | |||
| SRR14718101_2.fastq.gz | Fastqsanger.gz | |||
| SRR14718102_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
Similar Datasets
Project description:polyA RNA sequencing data generated from primary tail male adult fibroblasts in 4 cells states: proliferating, senescent, quiescent or immortalized and across two conditions: DMSO or MG132 treated were analyzed by RNA sequencing.
2022-09-20 | GSE176107 | GEO
Project description:How transcriptional regulators are linked to cell biological effectors of morphogenesis is not fully understood. To elucidate this linkage, we use the C. elegans male tail-tip as a model. The tail-tip is made of four cells that, in males, undergo changes in shape and position during the L4 stage. The transcription factor DMD-3 is the master regulator of this Tail-Tip Morphogenesis (TTM). To identify other genes involved in TTM, the lab has previously performed a genome-wide RNAi screen and conducted an RNA-seq differential expression (DE) analysis using tail tips isolated from L4 wild-type and dmd-3 mutant males. This yielded candidates for genes downstream of and regulated by DMD-3 directly or indirectly. To identify the direct targets of DMD-3, we conducted male-specific DMD-3 ChIP-seq on whole worms during TTM. We identified 1755 DMD-3 binding peaks representing 6061 genes and a de novo DMD-3-associated binding motif, sharing similarity to the chromatin binding factor, EOR-1. Integrating this data with the previous RNAi screen and the DE analysis, we found 270 candidates for direct DMD-3 targets in tail-tip cells. To validate these candidates, we inserted GFP into the endogenous loci using CRISPR and evaluated the expression of the fusion proteins. We then deleted the sequences associated with DMD-3 ChIP peaks or the DMD-3-associated binding motif and assessed if this resulted in a protein expression change or defective TTM. We found four genes where deletion of a peak had an effect: The transcription factor FOS-1 is expressed in nuclei of male tail tips during TTM and in the vulva. Deletion of a DMD-3 peak or DMD-3-associated motif sites abolishes expression in male tail-tip nuclei. NMY-2 is localized as a “cap” at the tip of the tail during TTM. Removal of the peak reduces the level of tail tip NMY-2 expression. The pan-1 locus has two peaks. PAN-1::GFP is first seen in puncta at the cell surface, then at basal lateral membranes. Removal of the distal peak causes TTM defects in 10% of screened males, while removal of both peaks leads to global, previously reported, pan-1 phenotypes. HMR-1 is expressed at adherens junctions at the onset of TTM and later forms puncta at the cell surface. Deleting the peak has little effect on expression but results in epidermal bulges in both sexes, including the mail tail region. Because of the global phenotypes observed in peak mutants, we hypothesize the peak regions contain binding sites for other factors. Additionally, using extrachromosomal arrays, we tested and confirmed the DMD-3-associated motif’s contribution to wild-type TTM.
2025-05-07 | GSE282566 | GEO
Project description:Control group: 250 g adult male rats injected with normal saline through tail vein; Experimental group: 250 g adult male rats injected with E. coli suspension through a tail vein
2024-06-13 | PXD053096 |
Project description:Transcriptional Control of C. elegans Male Tail Tip Morphogenesis by DMD-3
| PRJNA1189146 | ENA
Project description:Fibroblasts produce the majority of collagen in the heart and are thought to regulate extracellular matrix (ECM) turnover. However, the in vivo role of fibroblasts in structuring the basal ECM network is poorly understood. To examine the effects of fibroblast loss on the microenvironment in the adult murine heart, we generated mice with reduced fibroblast numbers and evaluated the tissue microenvironment during homeostasis and after injury. We determined that a 60-80% reduction in fibroblasts numbers did not overtly change the fibrillar collagen network but did alter the distribution and abundance of type VI collagen, a microfibrillar collagen that forms an open network with the basement membrane. In fibroblast ablated mice, myocardial infarction did not result in ventricular wall rupture, and heart function was more effectively preserved during angiotensin II/phenylephrine (AngII/PE) induced fibrosis. Analysis of cardiomyocyte contractility demonstrated weaker contractions and slower calcium release and reuptake in uninjured and AngII/PE infused fibroblast ablated animals. Moreover, fibroblast ablated hearts have a similar gene expression prolife to hearts with exercise-induced and physiological hypertrophy after AngII/PE infusion. These results suggest that hearts are resilient to a significant degree of fibroblast loss and that fibroblasts can directly impact cardiomyocyte function. Furthermore, a reduction in fibroblasts may have cardioprotective effects heart after injury suggesting that manipulation of the number of fibroblasts may have therapeutic value.
2023-03-10 | PXD021741 | Pride
Project description:Fibroblasts produce the majority of collagen in the heart and are thought to regulate extracellular matrix (ECM) turnover. However, the in vivo role of fibroblasts in structuring the basal ECM network is poorly understood. To examine the effects of fibroblast loss on the microenvironment in the adult murine heart, we generated mice with reduced fibroblast numbers and evaluated the tissue microenvironment during homeostasis and after injury. We determined that a 60-80% reduction in fibroblasts numbers did not overtly change the fibrillar collagen network but did alter the distribution and abundance of type VI collagen, a microfibrillar collagen that forms an open network with the basement membrane. In fibroblast ablated mice, myocardial infarction did not result in ventricular wall rupture, and heart function was more effectively preserved during angiotensin II/phenylephrine (AngII/PE) induced fibrosis. Analysis of cardiomyocyte contractility demonstrated weaker contractions and slower calcium release and reuptake in uninjured and AngII/PE infused fibroblast ablated animals. Moreover, fibroblast ablated hearts have a similar gene expression prolife to hearts with exercise-induced and physiological hypertrophy after AngII/PE infusion. These results suggest that hearts are resilient to a significant degree of fibroblast loss and that fibroblasts can directly impact cardiomyocyte function. Furthermore, a reduction in fibroblasts may have cardioprotective effects heart after injury suggesting that manipulation of the number of fibroblasts may have therapeutic value.
2023-03-10 | PXD021739 | Pride
Project description:In this study we investigated gene expression in tail fins of 12 samples. 3 samples from adult red-tailed male fish (MZCS002), 3 samples from adult yellow-tailed male fish (GRZ-BELL) and 3 samples each of the corresponding region in female fish of the same strain.
2025-11-09 | GSE190151 | GEO
Project description:The effect of a year-long 10 reduction in water temperature on global gene expression in tail skeletal muscle from adult, male zebrafish was determined using a long oligonucleotide probe set (16,399 65mers from Compugen) spotted onto glass slides. Outbred male zebrafish were obtained from a commercial supplier (Liles Tropical Fish, FL) at 6 months of age. Fish were maintained at 28 until 10 months of age. (see Gerhard et al., Exp Gerontol 37,1055-68, 2002) For temperature reduction, water temperature was decreased by 2.5 per week for 4 weeks. Fish were maintained until 22 months of age. Fish were fed fish flakes (Wardely Corp. Secaucus, NJ) twice per day. Each feeding was a discrete event in which a small measured amount of granular food was sprinkled on the water surface. A second small aliquot was offered if the first has been eaten within a few minutes. The feeding stopped when food from the previous aliquot has not been eaten and feeding behavior has ceased. By providing a consecutive series of small aliquots until food is no longer accepted, every member of the tank has an opportunity to eat until satiety, yet the amount of uneaten food is minimized. At 22 months of age, fish were euthanized by decapitation. Total RNA was harvested from a pool of tail muscle samples from 5 fish. Two independent pools of 5 fish per pool were collected from fish maintained at 18 and 28. Flip-dye hybridizations were performed on each pool for a total of 4 hybridizations in this study. Experiments DAR011d0001 and DAR011d0002 are flip-dye hybridizations from Pool 1. Experiments DAR011d0003 and DAR011d004 are flip-dye hybridizations from Pool 2.
2005-01-01 | E-TIGR-19 | biostudies-arrayexpress
Project description:scRNA-seq of pancreatic islets from adult male mice with Fltp-reporter sorting and pancreatic head-tail separation
| PRJNA872138 | ENA
Project description:Global investigation of the 3′ extremity of mRNA, despite its importance in gene regulation, has not been feasible due to technical challenges associated with homopolymeric sequences and relative paucity of mRNA. By developing a new methodology, TAIL-seq, we find a number of unforeseen features at the 3′ termini of mRNA. Our analyses reveal the transcriptome-wide distribution of poly(A) tail and estimate the median poly(A) length as 55-60 nt in mammalian cells, which is substantially shorter than generally conceived. Poly(A) length correlates with mRNA half-life but not with translation efficiency. Surprisingly, we find widespread uridylation and guanylation at the downstream of poly(A) tail. The U-tails are generally attached to short poly(A) tails (<25 nt) while the G-tails are found mainly on longer poly(A) tails (>40 nt), implicating their generic roles in mRNA stability control. In addition, TAIL-seq identifies, with a single nucleotide resolution, numerous nucleolytic events involved in microRNA processing and mRNA cleavage. Single replicate without any special experimental treatment for each of mouse fibroblast cell line NIH3T3 and human cervical cell line HeLa.
2014-02-28 | E-GEOD-51299 | biostudies-arrayexpress