|
| Status |
Public on Dec 18, 2019 |
| Title |
lncIRS2_NCD_2 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: liver
age_weeks: 18
genotype: wt
lna: lncIRS2 LNA
diet: NCD
|
| Treatment protocol |
Diet-induced obesity (DIO) was achieved by feeding a high-fat diet (HFD, D12492 (I) mod; Sniff) containing 22 kJ% carbohydrates, 24 kJ% protein and 54 kJ% fat from starting at 6-7-weeks-of-age. NCD (D12450B* mod LS; Sniff): containing 62 kJ% carbohydrates, 27 kJ% protein and 11 kJ% fat. Mice were injected for 12 weeks with control (Scr), Mafg or LncIRS2 LNA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Total RNA was isolated using peqGOLD TriFast (PEQLAB Biotechnologie).
Following initial quality checks, 1ug of total RNA of each sample was depleted for cytoplasmic and mitochondrial rRNA with Ribo-Zero Gold and strand-specific library preparation was performed using TruSeq RNA Gold Kit from Illumina. All libraries were sequenced in parallel on a HiSeq 4000 for 2 x 76 PE sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
SupplementaryData9_RNA-Seq[SCR_LNA_CD--LNCIRS2_LNA_CD].xlsx
|
| Data processing |
barcode and adapter removal using flexbar 3.4.0
computational rRNA depletion by filtering reads that map to known rRNAs in mice using Bowtie2 2.2.9
alignment of non-rRNA reads to the mm10 reference genome using STAR 2.6.0c
transcript assembly using cufflinks followed by cuffmerge
differential expression analysis using cuffdiff (Cufflinks suite 2.2.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx spreadsheet containing containing results of the transcript-level differential expression testing comparing two levels. Includes locus, FPKM values, log2FC as well as test statistics. For a complete description see https://cole-trapnell-lab.github.io/cufflinks/cuffdiff/
|
| |
|
| Submission date |
Oct 16, 2018 |
| Last update date |
Dec 18, 2019 |
| Contact name |
Jan Wilhelm Kornfeld |
| E-mail(s) |
janwilhelmkornfeld@bmb.sdu.dk
|
| Organization name |
University of Southern Denmark
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Noncoding Kornfeld Lab - Principles of Energy Homeostasis
|
| Street address |
Campusbej 50
|
| City |
Odense |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE121343 |
A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism: Liver RNA profiles of mice injected with control, Mafg and LncIRS2 LNA. |
| GSE121346 |
A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism. |
|
| Relations |
| BioSample |
SAMN10247481 |
| SRA |
SRX4893261 |
