|
| Status |
Public on Aug 01, 2018 |
| Title |
ΔMSN1 10h after lights off [dMSN1_10] |
| Sample type |
SRA |
| |
|
| Source name |
ΔMSN circadian time series
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: FGSC #11345
genotype/variation: msn-1 (NCU02671) knockout
time point: 10h after lights off
|
| Growth protocol |
Vogel's medium (1 X) supplemented with 2% glucose, 0.5% L-arginine and 10 ng/ml biotin was used as a standard growth medium. 200 ml medium in 500 ml flasks were inoculated with approximately 106 conidia and grown in light for six hours for conidial germination. Afterwards cultures were entrained in 11 hour/11 hour light/dark cycles for 2 days and released to constant dark for 22 hours. Cultures were transferred in a staggered manner, so harvesting of the cultures was performed within 10 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Triazol reagent and mRNA libraries were prepared with NEBNext Ultra RNA Library Prep Kit for Illumina in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBnext multiplex module.
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 |
processed data file: dMSN1_counts.csv
C5703ACXX_Dms1_44_66_14s008237-1-1_Ibberson_lane2Dms154_sequence
|
| Data processing |
Base calling using HiSeq Control Software (HCS) v2.2.38.
Transcript-level quantification using the pseudoalignment approach of kallisto (v 0.43.1) using kallisto quant -b 50 --single --rf-stranded -l 175 -s 20 --bias.
Counts extracted using tximport (v 1.4.0) with the gene level summarization with countsFromAbundance set to "scaledTPM".
Genome_build: NC12
Supplementary_files_format_and_content: comma-separated text file of read counts from scaled TPM values (unnormalized)
|
| |
|
| Submission date |
Apr 30, 2018 |
| Last update date |
Aug 01, 2018 |
| Contact name |
Michael Brunner |
| E-mail(s) |
michael.brunner@bzh.uni-heidelberg.de
|
| Phone |
+49 6221 54-4207
|
| Organization name |
Heidelberg University
|
| Department |
Biochemistry Center
|
| Lab |
Circadian Rhythms and Molecular Clocks
|
| Street address |
Im Neuenheimer Feld 328
|
| City |
Heidelberg |
| State/province |
Baden-Württemberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20705 |
| Series (1) |
| GSE113845 |
RNA-sequencing of WT and ΔMSN1 strains of N. crassa over a circadian time course |
|
| Relations |
| BioSample |
SAMN09000956 |
| SRA |
SRX4012500 |
