|
| Status |
Public on Mar 08, 2017 |
| Title |
Ldlr-Mc4r_chow_ko-ko_1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 6 months
tissue: Liver
genotype/variation: Ldlr-/- / Mc4r-/-
diet: regular chow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from liver tissue using TRI Reagent (TM) manufacturer's instructions
RNA libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 following the manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
reads were mapped using Tophat 2.0.6 and Bowtie2
alignment was filterd for mapping quality (samtools view -q 255) and all reads mapping to the mitochondrial genome were removed
readcounts were retrieved using BEDtools intersectBED
differential gene expression analysis was performed using the R-package Deseq
Genome_build: mm9
Supplementary_files_format_and_content: read counts are provided as matrix for all samples in a space delimited text file
|
| |
|
| Submission date |
Oct 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Torsten Schöneberg |
| Organization name |
Leipzig University
|
| Department |
Institute of Biochemistry, Medical Faculty
|
| Street address |
Johannisallee 30
|
| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE87743 |
Altered hepatic lipid metabolism in mice lacking both the melanocortin type 4 receptor and low density lipoprotein receptor |
|
| Relations |
| BioSample |
SAMN05879085 |
| SRA |
SRX2228930 |
