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Series GSE99245 Query DataSets for GSE99245
Status Public on Jan 23, 2018
Title The coding and noncoding transcriptome of Neurospora crassa
Organism Neurospora crassa
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary We present the NEUTRA database, a catalogue of the Neurospora transcriptome, based on RNA-Seq, RNAPII ChIP-Seq and ribosome fractionation studies.
The database also includes genome-wide binding sites of transcription factors involved in regulation of circadian gene expression.
In a comprehensive analysis of the transcriptome we identified and characterized 1478 long intergenic non-coding RNAs (lincRNAs) and 1056 natural antisense transcripts.
Both classes of long non-coding RNAs accumulate at lower levels than protein-coding mRNAs and they are considerably shorter.
We also confirmed annotated splice sites and identified new splice junctions and alternative splice sites, which are rare in Neurospora.
Our analysis revealed that the vast majority of lincRNAs and antisense transcripts do not contain introns.
NEUTRA is the first database to provide a collection of genome-wide deep sequencing data for the model organism Neurospora crassa and thus provides a tool that facilitates future research.
Overall design RNA-seq of Neurospora crassa.
Contributor(s) Cemel IA, Ha N, Schermann G, Yonekawa S, Brunner M
Citation(s) 29258423
Submission date May 24, 2017
Last update date Jul 25, 2021
Contact name Michael Brunner
Organization name BZH
Street address Im Neuenheimer Feld 328
City Heidelberg
ZIP/Postal code 69120
Country Germany
Platforms (3)
GPL16164 Illumina HiSeq 2000 (Neurospora crassa)
GPL17918 Illumina Genome Analyzer IIx (Neurospora crassa)
GPL20705 Illumina HiSeq 2500 (Neurospora crassa)
Samples (8)
GSM2637957 WT_constant dark
GSM2637958 WT_30 min light treatment
GSM2637959 WT_60 min light treatment
BioProject PRJNA387687
SRA SRP107924

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Supplementary file Size Download File type/resource
GSE99245_RAW.tar 76.7 Mb (http)(custom) TAR (of BIGWIG, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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