|
| Status |
Public on Sep 03, 2021 |
| Title |
RNAseq_VEH_3_5w |
| Sample type |
SRA |
| |
|
| Source name |
RNAseq_VEH_3_5w
|
| Organism |
Mus musculus |
| Characteristics |
tissue: visceral adipose tissue
status: VEH (active)
drosophila spike-in: NO
|
| Treatment protocol |
CORT mice were treated with corticosterone as described in PMID: 31117053.
|
| Growth protocol |
NA
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
ChIP-seq analysis: Alignment: Sequence reads of the samples with spike-in were mapped to a synthetic genome containing the mouse and the fruit fly chromosomes (mm9+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.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.bedgraph: Genome-wide ChIP-seq/RNA-seq.
Supplementary_files_format_and_content: *.bed: ChIP-seq peaks.
Supplementary_files_format_and_content: *.txt: Output files DESeq2 and DiffBind:
Supplementary_files_format_and_content: CORT-VEH_5W_results.txt: DESeq2 differential analysis
Supplementary_files_format_and_content: CORT-VEH_15W_results.txt: DESeq2 differential analysis
Supplementary_files_format_and_content: mouse_FPKMs.txt: FPKMs
Supplementary_files_format_and_content: H3K27ac_CORT5-VEH5_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27ac_CORT15_2-VEH15_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27ac_Peaks_CORT5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27ac_Peaks_VEH5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27ac_Peaks_VEH15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_CORT5-VEH5_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27me3_CORT15-VEH15_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27me3_Peaks_CORT5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_Peaks_CORT15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_Peaks_VEH5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_Peaks_VEH15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_CORT5-VEH5_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K4me3_CORT15-VEH15_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K4me3_Peaks_CORT5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_Peaks_CORT15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_Peaks_VEH5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_Peaks_VEH15_results.txt: DiffBind differential analysis vs. Input
|
| |
|
| Submission date |
Jul 07, 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 |
GPL13112 |
| Series (1) |
| GSE153934 |
Transcriptomic and epigenetic analysis of adipose tissue in Cushing Syndrome [mouse] |
|
| Relations |
| BioSample |
SAMN15463608 |
| SRA |
SRX8679848 |
