|
| Status |
Public on Aug 02, 2016 |
| Title |
MIHA HBx d14 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MIHA
transfection: C-terminal truncated HBx mutants (delta 14)
|
| Treatment protocol |
pcDNA6b-3xFLAG plasmids carrying empty vector alone, C-terminal truncated HBx d14 or C-terminal truncated HBx d35 were stably transfected into MIHA cells by Lipofectamine 2000 with stable cells selected using blasticidin
|
| Growth protocol |
MIHA liver cells were routinely cultured in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen Rneasy Mini Kit according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
To obtain high quality reads for downstream analysis, raw sequencing reads were firstly filtered for adapters sequences and low quality, in which more than 5% of the bases in a read contained unknown bases (‘N’) and more than 50% of the bases having a base quality value of ≤ 10, and were removed using cutadapt (Martin, 2011) and custom scripts. Subsequently, low complexity bases (more than 10bp of continuous bases of “A” and “T”) were trimmed from the 3’ end using prinseq (Schmieder and Edwards, 2011). Reads with length < 40bp were then discarded. Finally, sequencing reads were filtered for rRNA sequence and remaining high quality reads were used for downstream analysis.
The high quality reads were aligned against human transcriptome (hg19) using RSEM package v1.2.21 (Li and Dewey, 2011). Expression estimation and tests for differential expression were accomplished using EBSeq v1.6.0 (Leng at el, 2013) which is part of the RSEM package.
Genome_build: Human genome (hg19)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.
|
| |
|
| Submission date |
Aug 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chi Ho Lin |
| E-mail(s) |
nicklin.cpos@hku.hk
|
| Phone |
+852 2831 5511
|
| Organization name |
The University of Hong Kong
|
| Department |
Centre for PanorOmic Sciences
|
| Street address |
6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam
|
| City |
Hong Kong |
| ZIP/Postal code |
Hong Kong |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE71993 |
Differential gene expression profiling of MIHA cells transfected with C-terminal truncated HBx mutants |
|
| Relations |
| BioSample |
SAMN03983381 |
| SRA |
SRX1143532 |
