Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9983520.fastq.gz | Fastqsanger.gz | |||
| SRR9983530.fastq.gz | Fastqsanger.gz | |||
| SRR9983540.fastq.gz | Fastqsanger.gz | |||
| SRR9983550.fastq.gz | Fastqsanger.gz | |||
| SRR9983560.fastq.gz | Fastqsanger.gz |
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Project description:Deposition of intramuscular adipose tissue (IMAT; marbling) is one of the primary determinants for beef quality grade within the U.S. However, IMAT accumulation is often secondary to subcuta-neous (SCAT) and visceral (VIAT) adipose tissue deposition, which results in lower product yield. The mechanisms that underlie the differences in the accumulation of IMAT, SCAT, and VIAT are still not fully understood. The aim of this study was to define the depot-specific transcriptome and adipocyte function in IMAT, SCAT and VIAT in beef cattle. Functional transcriptome analysis in-dicated the activation of pathways for greater lipid accumulation and immune function in VIAT and SCAT compared with IMAT. Florescent activated cell sorting analysis identified a greater percentage of adipocyte stem and progenitor cells (ASPC) within IMAT compared to SCAT and VIAT, but lower ASPC's proliferation in vitro, suggesting potential functional defects on IMAT's adipogenic capacity. In vitro culture of adipocytes revealed greater lipid accumulation and insulin responses, and lower lipolysis of SCAT compared to IMAT adipocytes, with VIAT adipocytes having a characteristic of both SCAT, and IMAT adipocytes. Our findings revealed the de-pot-specific transcriptional profile of IMAT, SCAT and VIAT in beef cattle, which were corrobo-rated by differences on adipocyte metabolic function in vitro.
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Project description:RASA3 (RAS p21 protein activator 3), also called GAPIII or IP4BP (inositol 1,3,4,5-tetrakisphosphate, IP4, binding protein), is a member of the GAP1 family of RAS-GTPase-activating proteins (GAPs). The RAS superfamily of small GTPases includes the subfamily RAP. Small GTPases act as molecular switches, cycling between active GTP-bound and inactive GDP-bound forms. They are activated by guanine nucleotide exchange factors (GEFs), which stimulate GTP loading, and inactivated by GAPs, which accelerate GTP hydrolysis. A major role of RASA3 in hematopoiesis was first identified upon positional cloning of the co-isogenic autosomal recessive mouse mutation, scat (severe combined anemia and thrombocytopenia. The scat phenotype, in addition to severe anemia and thrombocytopenia, includes significant leukopenia as well. The scat disease progresses episodically, with periods of severe crisis interspersed with one or two periods of remission. The RASA3 mutation (G125V) in scat causes mislocalization of RASA3 to the cytosol, abrogating RASA3 GAP activity and increasing active RAS levels in scat erythroid cells. As part of a broader study to analyze the role of RASA3 in hematopoiesis, we performed RNAseq studies to generate hypotheses regarding the progression of the scat disease from periods of crisis to partial remission.
2021-02-10 | GSE148821 | GEO
Project description:Adult stem cells have unique properties in both proliferation and differentiation preference. However, the molecular mechanisms remain unclear. In this study, we hypothesized that the matrix microenvironment plays a critical role in the fate determination of local stem cells. Four rabbits were used to provide donor-matched adipose stem cells from either subcutaneous adipose tissue (ScAT) or infrapatellar fat pad (IPFP). Proliferation and multi-lineage differentiation were evaluated in adipose stem cells from donor-matched ScAT and IPFP. RNA sequencing (RNA-seq) and proteomics were conducted to uncover potential molecular mechanisms underlying the interaction between adipose stem cells and the local matrix microenvironment. We found that stem cells from ScAT exhibited significantly higher proliferation and adipogenic capacity compared to those from donor-matched IPFP while stem cells from IPFP displayed significantly higher chondrogenic potential compared to those from donor-matched ScAT. Our findings are strongly endorsed by supportive data from transcriptome and proteomics analyses, indicating that a unique extracellular matrix microenvironment is critical in the determination of local stem cell fate.
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Project description:Pediatric obesity prevalence is rapidly rising worldwide and “omic” approaches are helpful in obesity molecular pathophysiology investigation. This work aimed at the identification of transcriptional differences in subcutaneous adipose tissue (scAT) of children with overweight (OW), obesity (OB) or severe obesity (SV) respect those with normal weight (NW). Periumbilical scAT biopsies were collected from 20 male children aged 1-12 years. Considering BMI z-score, chil-dren were stratified into 4 groups: SV, OB, OW, NW. scAT RNA-Seq analyses were performed, differential expression analysis was achieved using the DESeq2 R package. Pathways analysis was performed to gain biological insights on gene expression. Our data highlight the significant deregulation in both coding and non-coding transcripts in the SV group when compared to NW, OW, and OB. KEGG pathway analysis showed involvement for coding transcripts mainly in li-pid metabolism. GSEA analysis revealed upregulation of lipid degradation and metabolism in SV vs OB and SV vs OW. Bioenergetic processes and the catabolism of branched-chain amino acids resulted upregulated in SV when compared to OB, OW, NW. In conclusion, we report for the first time that a significant transcriptional deregulation occurs in periumbilical scAT of children with severe obesity with respect to normal weight, overweight or mild obesity.
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Project description:Gray fox (Urocyon cinereoargenteus) and island fox (Urocyon littoralis) Raw sequence reads
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Project description:The present study was designed to identify determinants that foreshadow successful weight maintenance. More specifically, we examined whether subcutaneous adipose tissue (scAT) gene expression of participants who experience successful weight maintenance following caloric restriction differed from that of participants who regain weight. Forty women followed a dietary protocol consisting of an 8-week low calorie diet (LCD) and a 6-month weight maintenance phase. At the end of the protocol, participants were classified as weight maintainers (WM; 0-10% weight regain) and weight regainers (WR; 50-100% weight regain). Anthropometric measurements, plasma parameters, and scAT biopsies were taken before and after the LCD. Adipose tissue gene expression profiles were studied in all individuals before and after the LCD.
2011-09-29 | E-GEOD-24432 | biostudies-arrayexpress
Project description:The present study was designed to identify determinants that foreshadow successful weight maintenance. More specifically, we examined whether subcutaneous adipose tissue (scAT) gene expression of participants who experience successful weight maintenance following caloric restriction differed from that of participants who regain weight.
2011-09-30 | GSE24432 | GEO