|
| Status |
Public on Aug 10, 2019 |
| Title |
3_4h_mock_untreated |
| Sample type |
SRA |
| |
|
| Source name |
surrounding tissue from partial liver resection after recurrent hepatic metastasis
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
cells: primary human hepatocytes
inoculation: control
treatment: PBS
time point of rna extraction post inoculation: 4 h
|
| Treatment protocol |
Virus stock of HEVcc intracellular p6_G1634R was produced in HepG2 in DMEM complete with freeze and thaw cycles in DMEM complete. The virus was filtered through a 0.45 μm filter to remove all potential leftover cell debris. Afterwards virus was used for inoculation of the primary cells at an MOI of 1 and diluted – if necessary – in DMEM complete for the human primary cells (PHH). As a control 25 μM ribavirin was used.
|
| Growth protocol |
Primary human hepatocytes (PHH) were isolated from liver specimens, plated at a density of 1.3×10e6 on collagen-coated 6-well dishes, and kept in hepatocyte culture medium (Williams´ medium E)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from primary cells was extracted using a NucleoSpin RNA kit (Macherey-Nagel, Ref 740955.250) according to the manufacturer’s instructions. RNA quality was checked on an Agilent Bioanalyzer.
Libraries were prepared according to manufacturer's instructions accompanying the NEBNext Ultra II Directional RNA Library Prep Kit (#E7765S/L)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
3_4h_mock_untreated_S37
|
| Data processing |
RNA libraries were run on Illumina NovaSeq6000, basecalling was performed using Real-Time Analysis (RTA) v3.3.3
bcl files were converted to fastq files with bcl2fastq v2.20.0.422
Quality of fastq files was checked with CLC Genomics Workbench 11.0.1
mapping of fastq files to homo sapiens (hg 38) sequence and calculation of Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed using CLC Genomics Workbench 11.0.1 (Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0.8; Similarity fraction = 0.8)
Genome_build: hg38
|
| |
|
| Submission date |
Aug 09, 2019 |
| Last update date |
Aug 10, 2019 |
| Contact name |
Daniel Todt |
| E-mail(s) |
daniel.todt@rub.de
|
| Phone |
+492343222463
|
| Organization name |
Ruhr University Bochum
|
| Department |
Molecular & Medical Virology
|
| Street address |
Universitätsstr. 150
|
| City |
Bochum |
| ZIP/Postal code |
44801 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE135619 |
Robust hepatitis E virus infection and transcriptional response in human hepatocytes |
|
| Relations |
| BioSample |
SAMN12542184 |
| SRA |
SRX6686220 |
