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Sample GSM3121146 Query DataSets for GSM3121146
Status Public on Aug 01, 2018
Title ΔMSN1 8h after lights off [dMSN1_8]
Sample type SRA
 
Source name ΔMSN circadian time series
Organism Neurospora crassa
Characteristics strain: FGSC #11345
genotype/variation: msn-1 (NCU02671) knockout
time point: 8h 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_lane2Dms152_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 SAMN09000958
SRA SRX4012499

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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