|
| Status |
Public on Aug 08, 2023 |
| Title |
Rep_full_2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
cell type: EGFP+ Cd24+ Epcam+ cells
genotype: WT
treatment: AAV8-TBG-Cre injected; challenged with 0.1% DDC for 8 weeks
Stage: Rep_full
|
| Treatment protocol |
Mice were injected with AAV8-TBG-Cre for lineage trace hepatocytes. One week after AAV injection, biliary reprogramming was induced by challenging the mice with diet containing 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC). After 8 weeks, cells were harvested, FACS-sorted, and RNA was isolated from them.
|
| 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 |
T3412
|
| 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 |
Aug 08, 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) |
| GSE218945 |
Characterizing transcriptomic changes at different stage of hepatobiliary reprogramming in the adult mouse liver |
| GSE221225 |
Sox4 in adult hepatocytes |
|
| Relations |
| BioSample |
SAMN31899372 |
| SRA |
SRX18405970 |
