|
| Status |
Public on Dec 26, 2018 |
| Title |
Cp_2_0 |
| Sample type |
SRA |
| |
|
| Source name |
whole blood, all
|
| Organisms |
Candida parapsilosis; Homo sapiens |
| Characteristics |
c. parapsilosis strain: GA-1
time point: 0 minutes
|
| Treatment protocol |
Homo sapiens whole blood cells were treated with Candida parapsilosis GA-1.
|
| Growth protocol |
Candida parapsilosis cells grew at 37°C in Homo sapiens whole blood.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
To isolate human RNA aliquots of infected or mock infected samples were added to a PAXgene® Blood RNA Tube (PreAnalytiX) and processed with the PAXgene® Blood RNA Kit (PreAnalytiX) according to the manufacturer’s protocol. For fungal RNA isolation aliquots were added to ice-cold water, centrifuged and immediately frozen in liquid nitrogen. The cell pellet was further processed with the RiboPure™-Yeast Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. RNA quantity was determined with NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific) and RNA quality was verified with an Agilent 2100 Bioanalyzer (Agilent Technologies). Fungal and human RNA samples were pooled subsequently in a quantitative ratio of 1:10.
Library Preperation was performed by GATC Biotech using validated standard procedures modified to optimize the method for automated Preperation. Library Preparation consisted of the following steps: Purification of poly-A containing mRNA molecules, mRNA fragmentation, Random primed cDNA synthesis (strand specific), Adapter ligation and adapter specific PCR amplification
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RTA software version 1.18.64 were used for basecalling.
Read quality were checked with Fastqc. Reads were trimmed with trimmomatic version 0.32 and following parameters: SE threads 5 -phred33 FILE LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 15:20 MINLEN 30
Trimmed reads were mapped to reference genome of Candida parapsilosis CDC317_version_s01-m03-r10_features and of Homo sapiens GRCh38.77 using tophat2 with following parameters: -p 10 -g 1 --no-mixed --no-discordant --b2-very-sensitive --max-intron-length 100000 -o OUTDIR -G ANNOTATION INDEX FASTQFILE > OUTFILE
Mapped reads were counted using featureCounts version 1.4.5 and DeSeq2 were used for differential expression filtering.
Genome_build: GRCh38.77, CDC317_version_s01-m03-r10_features
Supplementary_files_format_and_content: Comma-delimited text files include counts for each gene per sample
|
| |
|
| Submission date |
May 08, 2018 |
| Last update date |
Dec 26, 2018 |
| Contact name |
Philipp Kämmer |
| E-mail(s) |
philipp.kaemmer@leibniz-hki.de
|
| Organization name |
Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)
|
| Department |
Microbial Pathogenicity Mechanisms
|
| Street address |
Adolf-Reichwein-Straße 23
|
| City |
Jena |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24976 |
| Series (2) |
| GSE114177 |
Homo sapiens whole blood infected with Candida spp. (here: Candida parapsilosis) |
| GSE114180 |
Homo sapiens whole blood infected with Candida spp. |
|
| Relations |
| BioSample |
SAMN09091372 |
| SRA |
SRX4053960 |
