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Sample GSM1849374 Query DataSets for GSM1849374
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
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
BioSample SAMN03983381
SRA SRX1143532

Supplementary file Size Download File type/resource
GSM1849374_MIHA_HBx_d14.txt.gz 387.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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