|
| Status |
Public on Nov 07, 2018 |
| Title |
WT_exp_2 |
| Sample type |
SRA |
| |
|
| Source name |
mycelium
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: MJK17.25 (derivative of MA169.4)
tissue: mycelium
age: exponential growth phase
genotype: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelium was sampled, flash frozen and grinded. RNA was extracted using TRIzol method from Vitrogen
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequenced libraries were mapped against predicted transcripts from A. niger CBS 513.88 genome (http://fungi.ensembl.org/) with STAR. Raw counts for reads mapping to unique exons were calculated with Bioconductor packages; GenomicFeatures and GenomicAlignments.
Normalization and differential gene expression analysis were performed with DEseq2.
|
| |
|
| Submission date |
Aug 31, 2018 |
| Last update date |
Nov 07, 2018 |
| Contact name |
Paul Schäpe |
| E-mail(s) |
paul.schaepe@tu-berlin.de
|
| Phone |
+493031472271
|
| Organization name |
TU-Berlin
|
| Department |
Applied and Molecular Microbiology
|
| Street address |
Gustav-Meyer-Allee 25
|
| City |
Berlin |
| ZIP/Postal code |
13355 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25519 |
| Series (1) |
| GSE119311 |
Comparative transcriptomics of Aspergillus niger when deleted or overexpressed for the putative transcription factors MjkA, MjkB and the histon deactelyase HdaX |
|
| Relations |
| BioSample |
SAMN09940777 |
| SRA |
SRX4628185 |
