NEUTRA (Neurospora crassa Transcriptome Tool)
Available tools
Search by Gene (available under "Tools" -> "Search by Gene"): Directs to a query window and a list of RNA-Seq and ChIP-Seq data sets. Corresponding data of the selected gene will be visualized on runtime.
Genome Browser (available under "Tools" -> "Genome Browser"): The genome browser was created by JBROWSE and uses the NC10 version of the N. crassa genome.
The list of the available experimental data is as follows:
| Experiment name | Experiment details | Publication |
|---|---|---|
| RNA-Seq Time Course (WT, 0-22 h after light to dark transfer) | WT (FGSC #2489); Cultures were entrained in 11 h/11 h light/dark cycles for 2 days and released to constant darkness for 22 h. Samples were harvested at 2 h intervals. | Sancar et al. (2015). BMC Biol. PubMed Central ID: PMC4381671 |
| RNA-Seq Time Course (Δcsp1, 0-22 h after light to dark transfer) | Δcsp1 (FGSC #11348); Cultures were entrained in 11 h/11 h light/dark cycles for 2 days and released to constant darkness for 22 h. Samples were harvested at 2 h intervals. | Sancar et al. (2015). BMC Biol. PubMed Central ID: PMC4381671 |
| RNA-Seq Light Induction (WT, 0-120 min after light exposure) | WT (FGSC #2489); Cultures were grown for 1 day in light at 25°C and transferred to darkness for 24 h before they were exposed to light (100 μE) and harvested after 0, 30, 60 and 120 min light exposure. | Sancar et al. (2015). PLoS Genet. PubMed Central ID: PMC4378982 |
| RNA-Seq Light Induction (Δsub1, 0-120 min after light exposure) | Δsub1 (FGSC #11127); Cultures were grown for 1 day in light at 25°C and transferred to darkness for 24 h before they were exposed to light (100 μE) and harvested after 0, 30, 60 and 120 min light exposure. | Sancar et al. (2015). PLoS Genet. PubMed Central PMCID: PMC4378982 |
| RNA-Seq Light Induction (Δff7, 0-120 min after light exposure) | Δff7 (FGSC #11073); Cultures were grown for 1 day in light at 25°C and transferred to darkness for 24 h before they were exposed to light (100 μE) and harvested after 0, 30, 60 and 120 min light exposure. | Sancar et al. (2015). PLoS Genet. PubMed Central ID: PMC4378982 |
| RNA-Seq (Δwc1 and Δwc2, constant light) | Δwc1 and Δwc2; mRNA was purified from light-grown cultures. | Unpublised |
| RNA-Seq (Δcsp1 and csp1 overexpression, constant light) | Δcsp1 (FGSC #11348), R1 (stable csp1 overexpressing strain); mRNA was purified from light-grown cultures. | Sancar et al. (2011). Mol. Cell PubMed Central ID: PMC22152473 |
| RNA-Seq Strand Specific Light Induction (WT, 0-120 min after light exposure) | WT (FGSC #2489); Cultures were grown for 1 day in light at 25°C and transferred to darkness for 24 h before they were exposed to light (100 μE) and harvested after 0, 30, 60 and 120 min light exposure. | Unpublished |
| RNAPII Ser2-P ChIP-Seq Time Course (WT, 0-22 h after light to dark transfer) | WT (FGSC #2489); Cultures were entrained in 11 h/11 h light/dark cycles for 2 days and released to constant darkness for 22 h. Samples were harvested at 2 h intervals. | Sancar et al. (2015). BMC Biol. PubMed Central ID: PMC4381671 |
| RNAPII N-terminus ChIP-Seq Double Light Pulse (WT, double light pulse at 0 and 30 min) | WT (FGSC #2489); Cultures were grown for 36 h in constant light and for 24 h in constant darkness before they were exposed to a 1-min low light-pulse (LP) (2 μE) and subsequently challenged with a high-LP (50 μmol m−2 s−1) 30 min after the first LP. Samples were collected at 0, 5, 30 and 35 min. | Cesbron et al. (2015). Nat. Commun. PubMed Central ID: 25851692 |
| RNAPII Ser5-P ChIP-Seq Double Light Pulse (WT, double light pulse at 0 and 30 min) | WT (FGSC #2489); Cultures were grown for 36 h in constant light and for 24 h in constant darkness before they were exposed to a 1-min low light-pulse (LP) (2 μE) and subsequently challenged with a high LP (50 μE) 30 min after the first LP. Samples were collected at 0, 5, 30 and 35 min. | Cesbron et al. (2015). Nat. Commun. PubMed Central ID: 25851692 |
| RNAPII Ser2-P ChIP-Seq Double Light Pulse (WT, double light pulse at 0 and 30 min) | WT (FGSC #2489); Cultures were grown for 36 h in constant light and for 24 h in constant darkness before they were exposed to a 1-min low light-pulse (LP) (2 μE) and subsequently challenged with a high LP (50 μE) 30 min after the first LP. Samples were collected at 0, 5, 30 and 35 min. | Cesbron et al. (2015). Nat. Commun. PubMed Central ID: 25851692 |