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| Status |
Public on Mar 10, 2021 |
| Title |
NW1_S1 |
| Sample type |
SRA |
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| Source name |
Subcutaneous Adipose Tissue
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| Organism |
Homo sapiens |
| Characteristics |
gender: female
age: age 37 ± 6.7 years
bmi: 24.3 ± 0.9 kg/m2
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| Treatment protocol |
The biopsy was immediately transferred to the laboratory and processed. A fragment of the whole adipose tissue biopsy was immediately frozen in liquid nitrogen for RNA extraction.
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| Growth protocol |
Biopsies of SAT were collected from a total of 20 subjects: 5 healthy normal weight women (CTRL, age 37 ± 6.7 years, BMI 24.3 ± 0.9 kg/m2), 5 obese women (OBF, age 41 ± 12.5 years, BMI 38.2 ± 4.6 kg/m2), 5 obese women with T2D (OBT2D; age 54.6 ± 14.9 years, BMI 38.1 ± 11.8 kg/m2) and 5 obese men (OBM, age 42.4 ± 6.58 years, BMI 36.9 ± 3.5 kg/m2). Each collected biopsy was weighed and stored in 1 ml of DMEM (Invitrogen Corporation, Jefferson City, MO) supplemented with 2.5% Bovine Serum Albumin (Sigma, St. Louis, MO) per gram of collected tissue.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 500 mg of frozen SAT was homogenized in RLT buffer (Qiagen). RNA from SAT was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer protocol and samples were then treated with the RNase-Free DNase Set (Qiagen). Concentration and quality of the extracted RNA were determined by the NanoDropH ND-1000 spectrophotometer (NanoDrop Technologies, USA) and RNA integrity verified by gel-electrophoresis.
RNA-seq libraries were prepared with the CORALL Total RNA-Seq Library Prep Kit (Lexogen) using 150 ng total RNAs from 5 healthy women, 5 obese women, 5 obese women with T2D and 5 obese men. The RiboCop rRNA Depletion Kit (Lexogen) was used to remove rRNA. Qualities of sequencing libraries were assessed with D1000 ScreenTape Assay using the 4200 TapeStation System (Agilent) and quantified with Qubit™ dsDNA HS Assay Kit (Invitrogen). RNA processing was carried out using Illumina NextSeq 500 Sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Transcript abundance was obtained using the BlueBee® Genomics Platform (Lexogen). Differential expression analysis for mRNA was performed using R package DESeq2
Genome_build: M24
Supplementary_files_format_and_content: BlueBee output:gene_ID, gene_name, locus, frags_locus, frags_expt, FPKM_THN, comp_frags_locus, comp_frags_expt, FPKM_CHN, status
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| Submission date |
Feb 02, 2021 |
| Last update date |
Mar 10, 2021 |
| Contact name |
Letizia Messa |
| E-mail(s) |
[email protected]
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| Organization name |
Politecnico di Milano
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| Department |
Electronics, Informatics and Bioengineering
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| Street address |
Piazza Leonardo Da Vinci 32
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| City |
Milan |
| ZIP/Postal code |
20133 |
| Country |
Italy |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE166047 |
Transcriptional deregulation in subcutaneous adipose tissue from severely obese patients is associated with cancer: focus on gender differences and role of type 2 diabetes |
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| Relations |
| BioSample |
SAMN17764965 |
| SRA |
SRX10008969 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5060703_NW1_S1.dat.gz |
1.5 Mb |
(ftp)(http) |
DAT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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