Ontology highlight
ABSTRACT:
PROVIDER: PRJNA955940 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Purpose: In this study, RNA-Seq was performed on intramuscular adipocytes and subcutaneous adipocytes at 0, 2, 4, and 8 days of differentiation to find genes and miRNAs that regulate the differentiation of two types of adipocytes. Methods: High-throughput sequencing was performed with NovaSeq 6000, and 150 paired-end reads were generated.Clean reads were filtered using HISAT2. The StringTie was used to assemble the transcript and calculate fragments per kilobase million mapped reads (FPKM) value. Results: We found 30 genes that mainly regulate the differentiation of subcutaneous adipocytes and 22 genes that mainly regulate the differentiation of subcutaneous intramuscular adipocytes. A total of 17 important candidate differential miRNAs were found, of which 4 miRNAs are believed to play a regulatory role in both types of cells, and 10 and 3 act on lipid deposition in subcutaneous and intramuscular adipocytes, respectively.
2022-06-07 | GSE193607 | GEO
Project description:Purpose: In this study, RNA-Seq was performed on intramuscular adipocytes and subcutaneous adipocytes at 0, 2, 4, and 8 days of differentiation to find genes and miRNAs that regulate the differentiation of two types of adipocytes. Method:The clean reads were mapped to the pig reference genome (scrofa. Sscrofa11.1) with perfect matches using Bowtie software. Annotated tRNA, rRNA, snoRNA, and snRNA sequences were filtered out, and conserved miRNAs were identified by the BLAST method against miRBase. The miRDeep2 software was used to predict new miRNAs based on the characteristics of the miRNA precursor hairpin structure. Differential expression analysis of two groups was performed using the DESeq2 R package. Differentially expressed miRNAs (DE-miRNAs) were screened with criterion of fold change > 1.5 and FDR < 0.05 using DESeq2. Target genes of DE-miRNAs were predicted by miRanda and targetscan. Results: We found 30 genes that mainly regulate the differentiation of subcutaneous adipocytes and 22 genes that mainly regulate the differentiation of subcutaneous intramuscular adipocytes. A total of 17 important candidate differential miRNAs were found, of which 4 miRNAs are believed to play a regulatory role in both types of cells, and 10 and 3 act on lipid deposition in subcutaneous and intramuscular adipocytes, respectively.
2022-06-07 | GSE193608 | GEO
Project description:RNA sequencing was performed to obtain a landscape of mRNA, circRNA, lncRNA, and miRNA of bovine intramuscular adipocytes in 4 differentiation periods.
2022-08-31 | GSE185850 | GEO
Project description:Bovine preadipocytes were isolated from subcutaneous fatty tissue and induced differentiation into adipocytes and RNAs were extracted from preadipocytes and adipocytes respectively. Small RNA-seq was performed by Beijing Genomics Institute biotechnology. A total of 250 differential expression miRNAs were screened, while 131 miRNAs were highly expressed in bovine adipocytes and 119 miRNAs were highly expressed in bovine preadipocytes. KEGG pathway analysis presented that 4.76% (p-value<0.001) differently expression genes enriched in lipid metabolism. GO analysis showed the target genes were mainly associated with cell process, cell and binding. Together these results provided important insights into the research of miRNAs for bovine preadipocytes differentiation.
2020-01-01 | GSE137993 | GEO
Project description:Bovine intramuscular adipocytes RNA-seq
| PRJNA770998 | ENA
Project description:*Background: Adipocytes mainly function as energy storage and endocrine cells. The amount and distribution of fat are important factor that influence the meat quality in the beef industry. Fat depot can be found around internal organ (ometal), beneath the skin (subcutaneous), and between muscles (intramuscular). Different adipose depot showed the biological and genetic difference depending on their location. This inter-depot variation might be influenced by the inherent genetic programing for development of adipose depots. In this study, we used RNA-seq data to investigate the difference in transcriptome of various adipose depots in Hanwoo. *Results: Using RNA-seq, we identified 5797, 2156, and 5455 DEGs in the comparison between OI, OS, and IS respectively (FDR<0.01) and found 853, 48, and 979 DEGs specific to subcutaneous, intramuscular and omental fat respectively. DEGs in intramuscular fat were highly enriched the metabolism related pathways compared to other fat depots. DEGs specific to the omental fat is significantly enriched in PPAR signaling pathway and cell-junction related pathway. In subcutaneous fat, cytokine-cytokine receptor interaction with chemokines (CXC and CC subfamily) was the most significantly enriched the pathways. Interestingly, melanogenesis pathway was associated with the subcutaneous depot. Even though the adipose tissues shared the same pathways for adipocyte differentiation, the regulation of genes were different based on the depot. *Conclusions: We comparatively analyzed the transcripome profile from different adipose tissues using NGS and identified DEGs between adipose depot and specific to depot in Hanwoo animals. The functional annotation analysis of DEGs found that transcriptome profile difference in various adipose tissue of intramuscular, subcutaneous, and ometal fat. whole mRNA sequencing profiles of nine Korean native cattle (nine profiles of omental fat tissue, nine profiles of intramuscular fat tissue, nine profiles of subcutaneous fat tissue and eight profiles of muscle tissue)
2013-07-25 | E-GEOD-39618 | biostudies-arrayexpress
Project description:We analyzed changes in the protein profiles that occur during differentiation and maturation of cultured human subcutaneous white preadipocytes. We divided the three cell lines (Cell Line-1, Cell Line-2, and Cell Line-3) of Caucasian-derived subcutaneous preadipocytes into five stages: i) subcutaneous preadipocytes as stage-1, ii) after inducing differentiation into adipocytes as stage-2, iii-v) from the initiation of lipid droplet formation to become mature subcutaneous adipocytes was defined as stage-3 to stage-5, depending on lipid droplet amount and formation. Proteins from the cells were extracted at each stage (stage-1 to stage-5), proteolytically cleaved using trypsin, and analyzed using untargeted liquid chromatography and mass spectrometry.
2022-07-04 | PXD035060 | JPOST Repository
Project description:*Background: Adipocytes mainly function as energy storage and endocrine cells. The amount and distribution of fat are important factor that influence the meat quality in the beef industry. Fat depot can be found around internal organ (ometal), beneath the skin (subcutaneous), and between muscles (intramuscular). Different adipose depot showed the biological and genetic difference depending on their location. This inter-depot variation might be influenced by the inherent genetic programing for development of adipose depots. In this study, we used RNA-seq data to investigate the difference in transcriptome of various adipose depots in Hanwoo. *Results: Using RNA-seq, we identified 5797, 2156, and 5455 DEGs in the comparison between OI, OS, and IS respectively (FDR<0.01) and found 853, 48, and 979 DEGs specific to subcutaneous, intramuscular and omental fat respectively. DEGs in intramuscular fat were highly enriched the metabolism related pathways compared to other fat depots. DEGs specific to the omental fat is significantly enriched in PPAR signaling pathway and cell-junction related pathway. In subcutaneous fat, cytokine-cytokine receptor interaction with chemokines (CXC and CC subfamily) was the most significantly enriched the pathways. Interestingly, melanogenesis pathway was associated with the subcutaneous depot. Even though the adipose tissues shared the same pathways for adipocyte differentiation, the regulation of genes were different based on the depot. *Conclusions: We comparatively analyzed the transcripome profile from different adipose tissues using NGS and identified DEGs between adipose depot and specific to depot in Hanwoo animals. The functional annotation analysis of DEGs found that transcriptome profile difference in various adipose tissue of intramuscular, subcutaneous, and ometal fat.
2013-07-25 | GSE39618 | GEO
Project description:To investigate the function lncFABP4 in the regulation of adipogenic differentiation, we overexpressed lncFABP4 in buffalo intramuscular adipocytes
2024-06-14 | GSE234915 | GEO
Project description:we collected tissues of subcutaneous fat and longissimus dorsi (LD) muscle from individuals that have divergent of backfat thickness and intramuscular fat content, and have similar age and body weight. The transcriptomic and proteomic data were gained using RNA-Seq and TMT to identify the key genes and pathways that specifically regulate the subcutaneous fat and intramuscular fat deposition in Dingyuan pig.
2022-04-04 | PXD027061 | Pride