|
| Status |
Public on Oct 05, 2023 |
| Title |
mice treated with CCl4 in combination with injection of AAV8-shRNA-lncHELF1#, biological rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mice treated with CCl4 in combination with injection of AAV8-shRNA-lncHELF1#, biological rep1
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c
tissue: liver
age: 8 weeks old
Sex: male
genotype: mice treated with CCl4 in combination with injection of AAV8-shRNA-lncHELF1#
|
| Treatment protocol |
For CCl4-induced mouse liver fibrosis model, the AAV8 virus was injected via the tail vein 4 weeks after the first injection of CCl4 (1x10`12 pfu/mouse) . After treatment with CCl4 for 8 weeks, all mice were sacrificed under anesthesia with 3% sodium pentobarbital (45 mg/kg, ip).
|
| Growth protocol |
8 weeks old Balb/c male background were used in CCl4-induced liver fibrosis model
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA of liver tissues were isolated useing Trizol reagent. Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer
The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
sh1_CCl4_1
|
| Data processing |
basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads"
Mapping clean reads to hg19 whole genome using BWA
Bowtie2 was used to get mapping ratio
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: TPM
|
| |
|
| Submission date |
Aug 19, 2021 |
| Last update date |
Oct 05, 2023 |
| Contact name |
Kun Zhang |
| E-mail(s) |
[email protected]
|
| Phone |
022-83336819
|
| Organization name |
Tianjin medical university
|
| Department |
Department of Histology and Embryology
|
| Street address |
Qixiangtai Road NO.22
|
| City |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE182485 |
Expression data that were specifically regulated by lncRNA-HELF (ENSMUST00000147617 ) in livers of mice undergoing CCl4-induced liver fibrosis |
|
| Relations |
| BioSample |
SAMN20864126 |
| SRA |
SRX11828895 |
