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| Status |
Public on May 31, 2022 |
| Title |
HepAD38 without DOX RNA-seq rep1 |
| Sample type |
SRA |
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| Source name |
HepG2 cell
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HepAD38
with dox or not: without DOX
hbv replication: Yes
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| Treatment protocol |
Change the medium to DMEM/F-12 containing ,10% tet-free FBS, PS, and G418, and allow the cells to propagate for 15 days.
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| Growth protocol |
Grow HepAD38 cells in a 10-cm plate with DMEM/F-12/ PS/G418/Dox.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China).RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Sequenced reads were removed adaptor and low-quality reads with cutadapt.
The remaining reads were mapped to human genome hg19 with hisat2 (version 2.1.0)
Transcript abundance values were quantified by htseq-count(Anders et al., 2015).
Differential expression analysis was performed with DESeq2 (Love et al., 2014).
To find the genes effected by the HBV cccDNA we selected the genes overlapped with the 4C reads, then visualized with the volcano plot (FDR<0.05 and log2(FC) > 1 as the cutoff)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq raw counts and DESeq2 results for each sample
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| Submission date |
Mar 06, 2020 |
| Last update date |
May 31, 2022 |
| Contact name |
Xiong Ji |
| E-mail(s) |
xiongji@pku.edu.cn
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| Organization name |
Peking University
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| Department |
School of life science
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| Lab |
Xiong Ji
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| Street address |
Yiheyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (2) |
| GSE146498 |
3D landscape of Hepatitis B virus interactions with human chromatins [RNA-seq] |
| GSE146499 |
3D landscape of Hepatitis B virus interactions with human chromatins |
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| Relations |
| BioSample |
SAMN14311046 |
| SRA |
SRX7859741 |
| 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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