|
| Status |
Public on Mar 20, 2023 |
| Title |
NASH2 |
| Sample type |
SRA |
| |
|
| Source name |
liver tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: liver tissue
with nash: Yes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAiso Plus Total RNA extraction reagent (Cat#9109, TAKARA)
VAHTS Stranded mRNA-seq Library Prep Kit for Illumina®（Cat#NR602-02，Vazyme）
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
NASH2 SYZ
|
| Data processing |
Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
Obtained clean reads were mapped to the mouse mm10 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models.
The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥2.
Genome_build: hg38
Supplementary_files_format_and_content: raw count and FPKM
|
| |
|
| Submission date |
Mar 20, 2020 |
| Last update date |
Mar 20, 2023 |
| Contact name |
Kangpeng Jin |
| E-mail(s) |
jinkangpeng@njmu.edu.cn
|
| Phone |
18502511055
|
| Organization name |
The Affiliated Drum Tower Hospital of Nanjing 9 University Medical School
|
| Department |
Department of Hepatobiliary Surgery
|
| Lab |
the Lab of Department of Hepatobiliary Surgery
|
| Street address |
321 Zhongshan Road
|
| City |
Nanjing |
| State/province |
Jiangsu Province |
| ZIP/Postal code |
210008 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE147304 |
RNA-Seq analylsis of human NASH and Normal liver tissues |
|
| Relations |
| BioSample |
SAMN14418357 |
| SRA |
SRX7963126 |
