|
| Status |
Public on Nov 28, 2023 |
| Title |
Hep_Sox4_3 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
cell type: Hepatocytes
genotype: Sox4
treatment: AAV8-TBG-HA-Sox4 (Sox4 expression vector) injected
|
| Treatment protocol |
Mice were injected with adeno-associated viruses (AAVs) packaged with mouse Sox4 expression vector (AAV8-TBG-HA-Sox4-P2A-Cre) or empty vector (AAV8-TBG-Cre). Hepatocytes were harvested 4 days post injection by a standard 2-step liberase digestion method followed by a Percoll enrichment step.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with Nucleospin RNA kit (Takara)
Library was prepared by Novogene (Sacramento, CA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
T3566
|
| Data processing |
Reads were mapped to GRCm39 mouse genome using the STAR aligner (version 2.7.10b).
Read counts were obtained using the featureCounts package (v2.0.1)
Read counts were imported to DESeq2, and normalization was performed using the "median of ratios normalization" method.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited normalized data including all the samples.
|
| |
|
| Submission date |
Nov 28, 2022 |
| Last update date |
Nov 28, 2023 |
| Contact name |
Takeshi Katsuda |
| E-mail(s) |
tkatsuda412@gmail.com
|
| Phone |
+1-215-746-5559
|
| Organization name |
University of Pennsylvania
|
| Department |
Perelman School of Medicine
|
| Lab |
Gastroenterology Division
|
| Street address |
421 Curie Blvd, BRB II/III Rm531
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE218947 |
Influence of Sox4 on transcriptomic changes in adult hepatocytes |
| GSE221225 |
Sox4 in adult hepatocytes |
|
| Relations |
| BioSample |
SAMN31899466 |
| SRA |
SRX18406152 |
