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| Status |
Public on Feb 28, 2017 |
| Title |
1Month-3 |
| Sample type |
SRA |
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| Source name |
liver tissue
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Liver
treatment: AAV8-1.2HBV
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| Treatment protocol |
AAV8-HBV1.2 vector was diluted into phosphate-buffered saline (PBS), and then 200 µl of rAAV8-HBV 1.2 vector [2×1011 vector genome equivalents (vg)] was injected into the mice via the tail vein. The control group was injected with the same volume of PBS. Liver tissues were collected at 1, 3 and 6-months post injection, and were frozen in liquid nitrogen.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA of each sample was extracted using a RNeasy Mini Kit (Qiagen).1μg of total RNA with a RIN value above 7 was used for following the library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument
pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data.
reference genome sequences and gene model annotation files of relative species were downloaded from genome website,ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al.
Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of genes were setted <0.05 to detect differential expressed ones.
Genome_build: mm9
Supplementary_files_format_and_content: exl files include RPKM values for all genes and the P-value of differentially expressed genes compared with HBV(-)mouse
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| Submission date |
Feb 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Fangming Kan |
| E-mail(s) |
kfm86@163.com
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| Organization name |
MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences
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| Street address |
Dongdansantiao
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| City |
Beijing |
| ZIP/Postal code |
100176 |
| Country |
China |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE95424 |
Transcriptome analysis of liver tissue in HBV - associated liver fibrosis mice |
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| Relations |
| SRA |
SRX2594759 |
| BioSample |
SAMN06472498 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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