|
| Status |
Public on Mar 30, 2022 |
| Title |
32_SC_WT |
| Sample type |
SRA |
| |
|
| Source name |
Hepatic stellate cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild-type
developmental stage: adult
tissue: unchallenged liver
cell type: Hepatic stellate cells
|
| Treatment protocol |
Mice expressing floxed alleles of Zeb2 with endothelial cell-specific Cre expression were treated with tamoxifen (2mg/day for 5 consecutive days) to delete Zeb2 in endotheilal cells; tamoxifen-treated littermates not expressing Cre were used as wild-type controls.
|
| Growth protocol |
Mice were housed under standard conditions with ad libitium access to water and chow. Mice were euthanized, the liver was isolated, digested and different liver cell types were isolated using density centrifugation/FACS, collected in lysis buffer and lysates were stored at -80ºC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Reliaprep (Promega) according to manurfacturer's protocol.
Illumina TruSeq stranded mRNA Library prep kit and resulting cDNA libraries were sequenced according to the Illumina TruSeq Rapid v2 protocol on an Illumina HiSeq2500 sequencer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Low quality reads and and contaminants (e.g. sequence adapters) were removed using Trimmomatic (version 0.32)
Sequences were aligned to the GRCm38 genome using HiSat2 (version 2.1.0)
Transcript abundance level (Transcript count) was generated using HTSeq (version 0.9.1)
The transcript counts were further processed using R software environment for statistical computing and graphics (version 3.4.0)
Differential expression was performed using edgeR R package using the negative binomial GLM approach
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files containing read counts per gene
|
| |
|
| Submission date |
May 15, 2020 |
| Last update date |
Mar 30, 2022 |
| Contact name |
Eskeatnaf Mulugeta |
| E-mail(s) |
[email protected]
|
| Phone |
0031646487835
|
| Organization name |
Erasmus University Medical Center Rotterdam (Erasmus MC)
|
| Department |
Cell Biology
|
| Street address |
Wytemaweg 80
|
| City |
Rotterdam |
| ZIP/Postal code |
3015CN |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE150699 |
Endothelial loss of Zeb2 distorts the hepatic angioarchitecture and aggravates liver fibrosis in mice |
|
| Relations |
| BioSample |
SAMN14934991 |
| SRA |
SRX8351066 |
