|
| Status |
Public on Oct 01, 2020 |
| Title |
DC-alone-4h |
| Sample type |
SRA |
| |
|
| Source name |
dendritic cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: dendritic cells
strainorline: DC
sampling time point (hours): 4
temperature: 37 degreeC
atmosphere: 5percent CO3
media: CellGro GMP serum-free DC medium
parameter: 260/280: 2.04
parameter: rin/rna integrity number: 8.5
parameter: concentration (ng/microliter): 67.36
parameter: volume (microliter): 65
|
| 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 single-end 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 15, Q25), 3’ ad 5’ quality clipping (Q3) and sequences with less than 30 bp were removed.
Read mapping was performed using HiSat2 with default parameters and -k 2.
Gene abunstance estimation (counting) was performed using featureCounts with default parameters.
Genome_build: GRCH38 89; Af293 s03-m05-r05
Supplementary_files_format_and_content: Gene abundance matrix was created by featureCounts based on the combined annotation of both organisms.
|
| |
|
| Submission date |
Aug 06, 2019 |
| Last update date |
Oct 01, 2020 |
| Contact name |
Bastian Seelbinder |
| E-mail(s) |
[email protected]
|
| 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 |
GPL18573 |
| Series (1) |
| GSE135450 |
Dual-RNA sequencing of dendritic cells challenged with Aspergillus fumigatus |
|
| Relations |
| BioSample |
SAMN12503019 |
| SRA |
SRX6660043 |
