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| Status |
Public on Jun 08, 2020 |
| Title |
RNAseq_Sub3_ABD |
| Sample type |
SRA |
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| Source name |
subcutaneous abdominal fat
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| Organism |
Homo sapiens |
| Characteristics |
body type: apple
cell type: adipocytes
fat depot: isolated from abdominal fat depot
Sex: female
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fat biospsies were collected, adipocytes were isolated by centrifugation and freeze at -80C. RNA was isolated using the GentleMACS Dissociator system (Milteny Biotec, GmbH, Germany). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Library preparation kit (Illumina Inc., San Diego, CA) as per the instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The RNA-Seq samples quality was checked using the tool FastQC. After this step, a required trimming was executed reducing distortions on the “per base sequence content” at the beginning of the reads using Trimmomatic. The trimmed samples were aligned to the UCSC genome, assembly hg19, using STAR. Reads were required to be uniquely mapped using Samtools for filtering, sorting and indexing. RSeQC was used to assess quality of each sample. The RNA sequencing abundance, raw read counts and TPM values, was calculated with TPMCalculator using the default parameters. The differential gene expression analysis was executed using the Bioconductor packages Deseq2 and EdgeR. An adjusted p-value of 0.05 and a logarithmic fold change of 1.5 was used to identified differentially expressed genes. All tools were executed using publicly available Common Workflows Language files and docker images with fixed tool versions
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include raw read count values and TPM values for each Sample
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| Submission date |
Jan 10, 2020 |
| Last update date |
Jun 08, 2020 |
| Contact name |
Adeline Divoux |
| E-mail(s) |
[email protected]
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| Phone |
4073037100
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| Organization name |
Adventhealth
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| Department |
Translational Research Institute
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| Street address |
301 E. Princeton St
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| City |
orlando |
| State/province |
FL |
| ZIP/Postal code |
32804 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE143448 |
Transcriptomic signatures and chromatin structure in adipocytes isolated from premenauposal women subcutaneous fat [RNA-seq] |
| GSE143450 |
Transcriptomic signatures and chromatin structure in adipocytes isolated from premenauposal women subcutaneous fat |
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| Relations |
| BioSample |
SAMN13825240 |
| SRA |
SRX7540668 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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