|
| Status |
Public on Sep 03, 2021 |
| Title |
Input_CTL |
| Sample type |
SRA |
| |
|
| Source name |
Input_CTL
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: visceral adipose tissue
chip antibody: none
status: CTL
drosophila spike-in: YES
|
| Treatment protocol |
Patients with tumoral adenocortical Cushing Syndrome and control patients matched by BMI, sex, age and cardiometabolic features.
|
| Extracted molecule |
genomic DNA |
| 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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)
|
| |
|
| 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 |
SAMN15496499 |
| SRA |
SRX8701076 |
