|
| Status |
Public on Apr 10, 2024 |
| Title |
rat injected with PBS rep3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: liver
strain: Sprague-Dawley rat
age: 5 months
genotype: wild type
treatment: PBS injection
|
| Treatment protocol |
Cirrhosis rats injected with PBS or HepLPCs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from liver tissue was isolated using TRIzol® Reagent (Invitrogen). DNase I (TaKara) was used to remove genomic DNA. The concentration and purity of RNA samples was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
Library preparation, and Illumina Hiseq xten/Nova seq 6000 Sequencing RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 10, 2022 |
| Last update date |
Apr 10, 2024 |
| Contact name |
hexin Yan |
| E-mail(s) |
yanhexin@renji.com
|
| Phone |
86-21-81875361
|
| Organization name |
Shanghai Reji Hospital
|
| Street address |
Pujian Road
|
| City |
Shanghai |
| ZIP/Postal code |
200120 |
| Country |
China |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE200550 |
Hepatocyte-derived liver progenitor-like cells attenuate liver cirrhosis via induction of apoptosis in hepatic stellate cells |
|
| Relations |
| BioSample |
SAMN27505555 |
| SRA |
SRX14801945 |
