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| Status |
Public on Sep 23, 2022 |
| Title |
RNA-Seq cpc-3 knockout DD28 rep2 |
| Sample type |
SRA |
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| Source name |
mycelia
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| Organism |
Neurospora crassa |
| Characteristics |
genotype: cpc-3 knockout
time point: DD28
replicate: 2
tissue: mycelia
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| Growth protocol |
Mycelial disks in Vogel’s minimal media containing 2% glucose (pH 6.0) were synchronized to the same time of day by a shift from 30°C constant light (LL) to 25°C constant dark (DD). The cultures were grown in LL for a minimum of 4 h and transferred to DD on day 1 (for collection at DD 36, 40, 44, 48, 52), day 2 (for collection at DD 12, 16, 20, 24, 28, 32), day 3 (for collection at DD8), and harvested either at 9:00 a.m. (DD 12, 16, 20, 36, 40, 44) or 5:00 p.m. (DD 8, 24, 28, 32, 48, 52) on day 3.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was harvested in the dark, pressed in between paper towels to remove excess media, and immediately frozen in liquid N2. polyA+ RNA was isolated from 100 μg of total RNA with NEB Oligo d(T)25 Magnetic Beads.
Purified mRNA (8 ng) was used as the input to generate RNA-seq libraries using the Lexogen SENSE Total RNA-seq Library Preparation Kit (Cat. #009).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
rs_dcpc3-2_28_HTS2652
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| Data processing |
For WT, Dfrq, and Dcpc-3 samples, basecalling was performed using the Real Time Analysis (RTA) workflow ver. 2.7.7. with default parameters. For cpc-3c samples, basecalling was performed using Illumina BaseSpace app using the FASTQ generation application ver. 1.0.0 and bcl2fastq.
RNA-seq reads were aligned to the N. crassa genome FungiDB Release 38 using STAR (Dobin et al, 2013).
Mapped RNA-seq reads were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) values using Cufflinks (Trapnell et al., 2010; 2012).
The RNA-seq time series was analyzed using the following Extended Circadian Harmonic Oscillation (ECHO, De Los Santos et al., 2019) settings: two unpaired replicates, smoothing function enabled, unexpressed genes excluded from the analysis at the default 70% threshold, and OE/RE cutoff of 1.25. Genes were considered rhythmic if they had Benjamini-Hochberg p-values < 0.05, and oscillation types harmonic, damped or forced.
Genome_build: N. crassa genome FungiDB Release 38
Supplementary_files_format_and_content: Output from Cufflinks in generic FPKM tracking format saved as plain text files containing the estimated gene-level expression values.
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| Submission date |
Aug 06, 2021 |
| Last update date |
Sep 25, 2022 |
| Contact name |
Deborah Bell-Pedersen |
| E-mail(s) |
dpedersen@bio.tamu.edu
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| Organization name |
Texas A&M University
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| Department |
Biology
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| Street address |
3258 TAMU
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| City |
College Station |
| State/province |
Texas |
| ZIP/Postal code |
77840 |
| Country |
USA |
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| Platform ID |
GPL30082 |
| Series (2) |
| GSE181564 |
Circadian Clock-Controlled Translation of Specific mRNAs in Neurospora crassa Requires Rhythmic eIF2α Activity and P-body Sequestration [RNA-seq] |
| GSE181566 |
Circadian Clock-Controlled Translation of Specific mRNAs in Neurospora crassa Requires Rhythmic eIF2α Activity and P-body Sequestration |
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| Relations |
| BioSample |
SAMN20601215 |
| SRA |
SRX11661778 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5506239_rs_dcpc3-2_28_HTS2652_genes_fpkm.txt.gz |
273.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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