|
| Status |
Public on Dec 08, 2022 |
| Title |
HepAD38 mRNA, DMSO, 7h, rep1 [s13] |
| Sample type |
SRA |
| |
|
| Source name |
HepAD38
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepAD38
cell type: Hepatocyte
treatment: DMSO
time: 7 hour
|
| Treatment protocol |
followed with DMSO or B02 (20 uM) treatment for 7 h. Total RNA was extracted by TRIzol.
|
| Growth protocol |
HepAD38 were cultured in the presence of 2 mM PFA from day 2 to day 6 after tet removal.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq tranded_mRNA Dual_Index library prep kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
The HiSeq Real Time Analysis software (RTA 1.18.64) was used for processing raw data files, the Illumina bcl2fastq2.17 was used to demultiplex and convert binary base calls and qualities to fastq format.
The sequencing reads were trimmed adapters and low quality bases using Cutadapt ( (version 1.18).
The trimmed reads were mapped to human reference genome (hg38) and GENCODE annotation v24 using STAR aligner (version 2.6.1) with two-pass alignment option.
RSEM (version 1.3.1) was used for gene and transcript quantification based on GENCODE v24 GTF file.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count and normalized RPKM values in gene count matrix file format for all samples
|
| |
|
| Submission date |
Jul 27, 2022 |
| Last update date |
Dec 08, 2022 |
| Contact name |
Ju-Tao Guo |
| E-mail(s) |
ju-tao.guo@bblumberg.org
|
| Phone |
2674321281
|
| Organization name |
Baruch S Blumberg Institute
|
| Street address |
3805 Old easton road
|
| City |
Doylestown |
| State/province |
PA |
| ZIP/Postal code |
18902 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE209863 |
Heat Shock Protein Family A Member 1 Promotes Intracellular Amplification of Hepatitis B Virus Covalently Closed Circular DNA |
|
| Relations |
| BioSample |
SAMN29992767 |
| SRA |
SRX16687779 |
