 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 21, 2018 |
| Title |
d06900GX1 |
| Sample type |
SRA |
| |
|
| Source name |
d06900GX
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: delta_fusR
tissue: Mycelium
|
| Growth protocol |
Conidia of Aspergillus niger strains MA234.1 and ΔfusR were grown as liquid shaken cultures at 200 rpm and 30 °C in 300 ml Transformation Medium + 1% glucose for 16 hours. Subsequently, the mycelium was transferred to 150 ml Minimal Medium + 25 mM xylose and grown for another 4 hours at 250 rpm and 30 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelium was flash-frozen in liquid nitrogen and ground using the TissueLyzer II (Qiagen, Venlo, The Netherlands). RNA was isolated using a standard TRIzol isolation procedure, followed by purification using the Nucleospin® RNA kit (Macherey-Nagel, Düren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
gene_exp.diff: d06900GX
Barcode: CGATGT
|
| Data processing |
Illumina Casava pipeline version 1.8.3 was used for base calling
The RNA-Seq pipeline used the TRIMMOMATIC read trimmer version 0.32 (Bolger et al., 2014) to remove low quality regions and the Illumina adapters from the reads
Tophat version 2.1.13 (Trapnell et al., 2009) was used to align sequence reads to the A. niger ATCC 1015 genome assembly
The program Cuffdiff (version 2.2.1), which is part of Cufflinks (Trapnell et al., 2010), was used to identify reads mapping to predicted genes and to identify differentially expressed genes.
Genome_build: Aspergillus niger ATCC 1015 v4.0 (http://genome.jgi.doe.gov/Aspni7/Aspni7.home.html)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
|
| |
|
| Submission date |
Jan 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Robin Ohm |
| E-mail(s) |
r.a.ohm@uu.nl
|
| Organization name |
Utrecht University
|
| Street address |
Padualaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21090 |
| Series (1) |
| GSE93990 |
The FlbA-regulated transcription factor FusR of Aspergillus niger is involved in production of fumonisin |
|
| Relations |
| BioSample |
SAMN06251702 |
| SRA |
SRX2512492 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
