SnRNA-seq data on human subcutaneous and omental white adipose tissue
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA937185 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23565800_1.fastq.gz | Fastqsanger.gz | |||
| SRR23565800_2.fastq.gz | Fastqsanger.gz | |||
| SRR23565801_1.fastq.gz | Fastqsanger.gz | |||
| SRR23565801_2.fastq.gz | Fastqsanger.gz | |||
| SRR23565802_1.fastq.gz | Fastqsanger.gz |
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Project description:We generated single nucleus transcriptomic atlas for human subcutaneous and omental white adipose tissue (WAT).
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Project description:This SuperSeries is composed of the following subset Series: GSE29409: Subcutaneous and omental white adipose tissue biopsies analysed from five obese patients GSE29410: Subcutaneous and omental white adipose tissue biopsies analysed from three obese patients Refer to individual Series
2012-01-01 | E-GEOD-29411 | biostudies-arrayexpress
Project description:The objective was to characterize differences in the secretome of human omental compared with subcutaneous adipose tissue using global gene expression profiling. Gene expression was measured using Affymetrix microarrays in subcutaneous and omental adipose tissue (n=3 independent subjects; 6 arrays). Predictive bioinformatic algorithms were employed to identify those differentially expressed genes that code for secreted proteins and to identify common pathways between these proteins. All patients provided informed written consent before inclusion in the study which was approved by the North of Scotland Research Ethics Committee (NOSREC). The subcutaneous and omental white adipose tissue biopsies were analysed from three obese patients (BMI 39.1+/-1.9 kg/m2; age 36 +/- 8 years) who had fasted overnight. Subcutaneous and omental white adipose tissue biopsies were taken at the time of surgery for vertical banded gastroplasty from n=3 independent subjects who had fasted overnight. (6 arrays). Adipose tissue samples were obtained within 5 minutes of the tissue being extracted from the patients and frozen immediately in liquid nitrogen. Subjects had fasted overnight prior to surgery. Total RNA was extracted using the RNeasy Lipid tissue mini kit followed by incubation with RNase free DNase (Qiagen, Crawley, West Sussex) for DNA-free RNA, following the manufacturer's instructions (Qiagen, Crawley, West Sussex). RNA was quantified on the Agilent 2100 Bioanalyser (Agilent Technologies, South Queensferry, West Lothian). This also shows the quality of the RNA extracted from the tissues. Only RNA showing no degradation (RIN greater than 9.0) was processed further. The DNA-free RNA from the subcutaneous and omental adipose tissue samples from the patients was then sent to a commercial company for analyses. The RNA from three volunteers (6 arrays ) was fragmented and hybridised to Human Affymetrix U133 plus 2 (Santa Clara, CA) gene chips following the Affymetrix protocol by the MRC Geneservice (MRC HGMP Resource centre, Babraham, Cambridge). Briefly, the Affymetrix one-cycle target labelling and control reagents were used to synthesize Biotin-labelled cRNA. The concentration of the cRNA was measured using a Nanodrop (Thermoscientific) and Agilent bioanalyser to rule out the possibility that only very short cRNA products were formed. This could have caused a 3’-5’ bias and influenced the data analysis. Approximately 20µg cRNA was used for further fragmentation and finally 10µg was used for the hybridisations. The Affymetrix protocols were followed for the hybridisations, washing, staining and scanning of the chips
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Project description:The objective was to characterize differences in the secretome of human omental compared with subcutaneous adipose tissue using global gene expression profiling. Gene expression was measured using Affymetrix microarrays in subcutaneous and omental adipose tissue (n=5 independent subjects; 10 arrays). Predictive bioinformatic algorithms were employed to identify those differentially expressed genes that code for secreted proteins and to identify common pathways between these proteins. The time course data was not included in the publication and has yet to be published. Patients undergoing surgery were weight stable one month prior to the operation and were not on any medication. All patients provided informed written consent before inclusion in the study which was approved by the North of Scotland Research Ethics Committee (NOSREC). The subcutaneous and omental white adipose tissue biopsies were analysed from five obese patients (BMI 44.5 +/-10 kg/m2; age 42.7 +/- 10 years) who had fasted overnight. Subcutaneous and omental white adipose tissue biopsies were taken at the time of surgery for vertical banded gastroplasty from n=5 independent subjects who had fasted overnight. (10 arrays). Further subcutaneous adipose tissue samples were taken at approximately four months post vertical banded gastroplasty surgery as the volunteers actively lost weight and at 12 months when the volunteers became weight stable (n=5 independent subjects, three time points 0, 4, and 12 months; 15 arrays). Therefore we report on 20 arrays in total including the arrays used to analyse the omental adipose tissue. Adipose tissue samples were obtained within 5 minutes of the tissue being extracted from the patients and frozen immediately in liquid nitrogen. Subjects had fasted overnight prior to surgery. Total RNA was extracted using the RNeasy Lipid tissue mini kit followed by incubation with RNase free DNase (Qiagen, Crawley, West Sussex) for DNA-free RNA, following the manufacturer's instructions (Qiagen, Crawley, West Sussex). RNA was quantified on the Agilent 2100 Bioanalyser (Agilent Technologies, South Queensferry, West Lothian). This also shows the quality of the RNA extracted from the tissues. Only RNA showing no degradation (RIN greater than 9.0) was processed further. The DNA-free RNA from the subcutaneous and omental adipose tissue samples from the patients was then sent to a commercial company for analyses. The RNA from five volunteers (20 arrays ) was fragmented and hybridised to custom Human NuGo (Nutrigenomics; http://www.nugo.org/everyone/35788) Affymetrix (Santa Clara, CA) gene chips HS 1a520180 following the Affymetrix protocol by Service XS (Leiden, The Netherlands). Briefly, the Affymetrix one-cycle target labelling and control reagents were used to synthesize Biotin-labelled cRNA. The concentration of the cRNA was measured using a Nanodrop (Thermoscientific) and Agilent bioanalyser to rule out the possibility that only very short cRNA products were formed. This could have caused a 3’-5’ bias and influenced the data analysis. Approximately 20µg cRNA was used for further fragmentation and finally 10µg was used for the hybridisations. The Affymetrix protocols were followed for the hybridisations, washing, staining and scanning of the chips
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Project description:The objective was to characterize differences in the secretome of human omental compared with subcutaneous adipose tissue using global gene expression profiling. Gene expression was measured using Affymetrix microarrays in subcutaneous and omental adipose tissue (n=3 independent subjects; 6 arrays). Predictive bioinformatic algorithms were employed to identify those differentially expressed genes that code for secreted proteins and to identify common pathways between these proteins. All patients provided informed written consent before inclusion in the study which was approved by the North of Scotland Research Ethics Committee (NOSREC).
2012-01-01 | GSE29410 | GEO
Project description:The objective was to characterize differences in the secretome of human omental compared with subcutaneous adipose tissue using global gene expression profiling. Gene expression was measured using Affymetrix microarrays in subcutaneous and omental adipose tissue (n=5 independent subjects; 10 arrays). Predictive bioinformatic algorithms were employed to identify those differentially expressed genes that code for secreted proteins and to identify common pathways between these proteins. The time course data was not included in the publication and has yet to be published. Patients undergoing surgery were weight stable one month prior to the operation and were not on any medication. All patients provided informed written consent before inclusion in the study which was approved by the North of Scotland Research Ethics Committee (NOSREC).
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Project description:The association between central obesity and insulin resistance reflects the properties of visceral adipose tissue. Our aim was to gain further insight into this association by analysing the lipid composition of subcutaneous and omental adipose tissue in obese women with and without insulin resistance. Subcutaneous and omental adipose tissue and serum were obtained from 29 obese nondiabetic women, 13 of whom were hyperinsulinemic. Histology, and lipid and gene profiling were performed. In omental adipose tissue of obese, insulin-resistant women, adipocyte hypertrophy and macrophage infiltration were accompanied by an increase in GM3 ganglioside and its synthesis enzyme ST3GAL5; in addition, phosphatidylethanolamine (PE) lipids were increased and their degradation enzyme, PEMT, decreased. ST3GAL5 was expressed predominantly in adipose stromovascular cells and PEMT in adipocytes. Insulin resistance was also associated with an increase in PE lipids in serum. Total RNA was isolated and up to 400 ng of total RNA per sample was labelled and hybridized to Illumina HumanHT-12_V4 expression BeadChip platform. Paired subcutaneous and omental samples from 6 women were analysed.
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Project description:To provide a comprehensive understanding of how GC affect adipose tissue and adipocyte function, we analyzed patterns of gene expression after culture of abdominal subcutaneous (sc) and omental (Om)) Adipose tissue of severely obese subjects (3F, 1M) in the presence of insulin or insulin (7 nM) plus dexamethasone (dex, 25 nM) for 7d.
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Project description:snRNA-Seq from Younger and Older human abdominal subcutaneous white adipose tissue
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