Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1054534 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27283710_1.fastq.gz | Fastqsanger.gz | |||
| SRR27283710_2.fastq.gz | Fastqsanger.gz | |||
| SRR27283719_1.fastq.gz | Fastqsanger.gz | |||
| SRR27283719_2.fastq.gz | Fastqsanger.gz | |||
| SRR27283720_1.fastq.gz | Fastqsanger.gz |
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Project description:Comparative transcriptome analysis of various adipose depots in Hanwoo
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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:Here we have employed chromatin immunoprecipitation combined with deep sequencing to map and compare PPARM-NM-3 binding in in vitro differentiated primary mouse adipocytes isolated from epididymal, inguinal, and brown adipose tissues. While these PPARM-NM-3 binding profiles are overall similar, there are clear depot-selective binding sites. Most PPARM-NM-3 binding sites previously mapped in 3T3-L1 adipocytes can also be detected in primary adipocytes, but there are a large number of PPARM-NM-3 binding sites that are specific to the primary cells, and these tend to be located in closed chromatin regions in 3T3-L1 adipocytes. The depot-selective binding of PPARM-NM-3 is associated with highly depot-specific gene expression. This indicates that PPARM-NM-3 plays a role in the induction of genes characteristic of different adipocyte lineages and that preadipocytes from different depots are differentially preprogrammed to permit PPARM-NM-3 lineage-specific recruitment even when differentiated in vitro. Examination of PPARM-NM-3 binding in in vitro differentiatied adipocytes isolated from three different adipose depots.
2012-10-11 | E-GEOD-41481 | biostudies-arrayexpress
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Project description:We performed RNA sequencing on the sorted adipose stem cells (ASCs) from multiple white adipose tissue depots to analyze the differential expression and pathway enrichment analysis of adipose stem cells from different anatomical sites.
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Project description:Considerable heterogeneity exists amongst adipose progenitor cells derived from primary visceral white adipose tissue depots. Single cell RNA sequencing, and state of the art analyses, have the power to disentangle this heterogeneity and reveal the underlying development processes that drive adipocyte maturation.
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Project description:Purpose : To understand differences in microRNA (miRNA) signatures of different adipose tissue depots to gain mechanistic insight regarding their contribution to metabolic disorders in obesity. Method : We performed small RNA-sequencing of brown, subcutaneous and visceral adipose depots from high fat diet-fed mice (mice were fed a 45% kcal fat diets from 5-6 weeks of age for 11 weeks). The main animal study reference: Kalupahana et al., J. Nutr, 2010 Results:Using the Gunaratne Next Generation pipeline (published in Creighton et al. 2009) miRNA expression profiles were identified. Counts of each unique read were normalized to total usable reads, and had 40 counts added. We mapped about 13.8 million sequence reads per sample to the Mus musculus genome (build mm 10). Altogether 1251 miRNAs were identified in three adipose tissues and out of which 246 showed differential expression with 1.25 or more fold change and p value <0.05 in one or more of the pairwise comparisons of the 3 adipose depots. Hierarchical clustering, demonstrated that biological replicates behaved appropriately as they were clustered together. BAT exhibited a different gene/ miRNA expression pattern than the 2 other WATs (SAT and VAT). SAT and VAT showed a closer relationship with each other than with BAT Conclusion : High fat diet differentially regulate specific miRNAs expression in different adipose tissue depots
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