|
Status |
Public on Sep 03, 2021 |
Title |
RNAseq_CS_HVC09 |
Sample type |
SRA |
|
|
Source name |
RNAseq_CS_HVC09
|
Organism |
Homo sapiens |
Characteristics |
tissue: visceral adipose tissue status: CS drosophila spike-in: NO
|
Treatment protocol |
Patients with tumoral adenocortical Cushing Syndrome and control patients matched by BMI, sex, age and cardiometabolic features.
|
Extracted molecule |
total RNA |
Extraction protocol |
For RNAseq: RNA was extracted using RNeasy Lipid Tissue Mini kit (Qiagen). For ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013). Libraries were prepared according to Illumina instructions.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
ChIP-seq analysis: Alignment: Sequence reads of the samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1. Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles with spike-in were normalized by the total number of fly reads of each sample. RNA-seq analysis: Alignment: Sequence reads were mapped against the hg19 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. Genome_build: hg19 Supplementary_files_format_and_content: Files *.bedgraph.gz (BedGraph, genome-wide ChIP-seq/RNA-seq)
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|
|
Submission date |
Jul 09, 2020 |
Last update date |
Sep 03, 2021 |
Contact name |
Mar Gonzalez-Ramirez |
E-mail(s) |
mar.bellvisgonzalez@gmail.com
|
Organization name |
Center for Genomic Regulation (CRG)
|
Street address |
C/ Dr Aiguader 88
|
City |
Barcelona |
ZIP/Postal code |
08003 |
Country |
Spain |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE140126 |
Transcriptomic and epigenetic analysis of adipose tissue in Cushing Syndrome [human] |
|
Relations |
BioSample |
SAMN15496493 |
SRA |
SRX8701038 |