|
| Status |
Public on Oct 01, 2020 |
| Title |
Donor3_08_DC_plus_CMV_2h |
| Sample type |
SRA |
| |
|
| Source name |
dendritic cells
|
| Organisms |
Homo sapiens; Human betaherpesvirus 5 |
| Characteristics |
cell type: dendritic cells
strainorline: DC; Human herpesvirus 5 strain TB40/E clone TB40-BAC4
number of fungal organisms (moi): --
samplingtimepoint (hours): 9
temperature: 37
atmosphere: 5% CO2
compound: Human herpesvirus 5 strain TB40/E clone TB40-BAC4
media: CellGro GMP serum-free DC medium
260/280: 2.27
rin/rna integrity number: 8.5
concentration (ng/ul): 16.25
volume (ul): 60
kit: RiboPure RNA purification kit
library_strategy: adapter ligation; strand specific
|
| Growth protocol |
CellGro GMP serum-free DC medium for up to 9h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA has been extracted and purified using the RiboPure RNA purification kit. Fragments were sequenced using Sequencing by synthesis (Illumina NextSeq 500).
RNA libraries were prepared for strand-specific sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality and adapter trimming were performed using Trimmomatic version 0.36, including windows size trimming (size 10, Q25), 3’ ad 5’ quality clipping (Q5) and sequences with less than 30 bp were removed.
Read mapping was performed using HiSat2 with default parameters.
Gene abunstance estimation (counting) was performed using featureCounts with default parameters.
Genome_build: GRCH38 89; Af293 s03-m05-r09; Human herpesvirus 5 strain TB40E clone TB40-BAC4
Supplementary_files_format_and_content: Gene abundance matrix was created by featureCounts based on the combined annotation of all 3 organisms.
|
| |
|
| Submission date |
Jul 16, 2019 |
| Last update date |
Oct 01, 2020 |
| Contact name |
Bastian Seelbinder |
| E-mail(s) |
bastian.seelbinder@leibniz-hki.de
|
| Organization name |
Hans-Knoell-Institute Jena
|
| Department |
Systems Biology and Bioinformatics
|
| Street address |
Adolf-Reichwein-Straße 23
|
| City |
Jena |
| ZIP/Postal code |
07747 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24958 |
| Series (1) |
| GSE134344 |
Triple-Sequencing of dendritic cells coinfected with Aspergillus fumigatus and cytomegalovirus |
|
| Relations |
| BioSample |
SAMN12284663 |
| SRA |
SRX6451440 |
