|
| Status |
Public on Nov 24, 2015 |
| Title |
B30 r1 |
| Sample type |
SRA |
| |
|
| Source name |
Mycelium
|
| Organism |
Aspergillus fumigatus |
| Characteristics |
strain: ATCC46645
tissue: Mycelium
growth condition: Human Blood
experiment: Blood7_1
|
| Treatment protocol |
Mycelia were split in tubes with convenient media (Blood or Minimal) or directly frozen in liquid nitrogen (pre). There are 2 biological replicates per condition (experiments Blood5 and Blood7 1, from different blood extractions). They were several times inverted and incubated on a rotator at 37°C for 15, 30, 60, 90, 180 min followed by harvesting and shock freezing in liquid nitrogen.
|
| Growth protocol |
A. fumigatus was grown 16 h in minimal medium, harvested and pooled.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
A. fumigatus mycelia was disrupted by grinding with liquid nitrogen, and total RNA was extracted with RNeasy plant (Qiagen, Germany)
RNA libraries were prepared for sequencing by GATC Biotech (Konstanz, Germany). using two different methods. For replicate 1, the time point pre, B30 and B180 the SMART protocol was used and for r1 M30 and M180 and all r2 time points the TrueSeq protocol was used. Paired end sequencing (Read length 100 bp) was carried out on Illumina HiSeq 2000 by GATC Biotech.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
FastQC tool was used to check the quality of the sequencing reads.
TopHat software was used to map the reads to the A. fumigatus reference genome (strain Af293, version 14) downloaded from EnsemblFungi website.
htseq-count tool was used in order to obtain the number of reads mapped to annotated genes.
Counts were normalized to RPKM values and ASCA method was used to remove the batch effect from the data
The NOISeq method was applied on the batch-corrected data to compute differential expression.
Genome_build: Af293
Supplementary_files_format_and_content: text file including RPKM values
|
| |
|
| Submission date |
Jun 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sonia Tarazona |
| E-mail(s) |
[email protected]
|
| Organization name |
Centro de Investigación Príncipe Felipe
|
| Lab |
Genomics of Gene Expression Lab
|
| Street address |
Eduardo Primo de Yúfera
|
| City |
Valencia |
| ZIP/Postal code |
46012 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18295 |
| Series (1) |
| GSE70227 |
Aspergillus fumigatus in blood reveals a "just wait and see" resting stage behavior |
|
| Relations |
| BioSample |
SAMN03792074 |
| SRA |
SRX1071024 |
