|
| Status |
Public on May 01, 2020 |
| Title |
VPA_OCA2 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: liver
age: 16 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA standard kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Analysis: NGS two group analysis with EdgeR . Feature level: gene. Data Column Used: est_counts.
Method: glm using secondary factor. Statistical Model: used provided second factor. Comparison: VPA_OCA-over-VPA.
Normalization: TMM. Differential expression test: QL. Log2 signal treshold: 4.322. Linear signal treshold: 20.
Genome_build: GRCm38.p5 (Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_91-2018-02-26)
Supplementary_files_format_and_content: tab-delimited text files include normalized count and FPKM (Fragments Per Kilobase Million) for each Sample
|
| |
|
| Submission date |
Oct 14, 2019 |
| Last update date |
May 01, 2020 |
| Contact name |
Evelin Krajnc |
| E-mail(s) |
[email protected]
|
| Organization name |
University Hospital Zürich
|
| Department |
Department of Clinical Pharmacology and Toxicology
|
| Street address |
Rämistrasse 100
|
| City |
Zürich |
| ZIP/Postal code |
8091 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE138810 |
Role of Farnesoid X Receptor (FXR) in Valproic acid-induced Hepatotoxicity |
|
| Relations |
| BioSample |
SAMN13025234 |
| SRA |
SRX6986468 |
