|
| Status |
Public on Dec 03, 2018 |
| Title |
0.5h |
| Sample type |
SAGE |
| Anchor |
NlaIII
|
| Tag Count |
925031 |
| Tag Length |
22 |
| |
|
| Source name |
0.5h after light exposure (after 6-days cultivation in dark)
|
| Organism |
Coprinopsis cinerea |
| Characteristics |
light length: 0.5h
strain: #326 (AmutBmut)
developmental stage: mycelia
|
| Treatment protocol |
Fluorescent light was exposed to mycelia for 0.5, 1 and 3h. The mycelia were harvested by excising the mycelial colony edge with a knife and scraping it gently off the cellophane sheet. Then immediately freezing them in liquid nitrogen. The collection of mycelia at the hyphal knot region was carried out under red light.
|
| Growth protocol |
Coprinopsis cinerea strain #326 was inoculated on edge of petri dish, and cultured on MY1/2G (Molt extract, Yeast extract, 0.2% glucose) for 6 day in dark at 28˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNAs for Super-SAGE were obtained from these mycelia using RNeasy Plant Mini kit (QIAGEN GmbH, Germany). The reagent of the kit (Buffer RLC) was added first to the frozen tissue, and the tissue was crushed in liquid nitrogen. The remaining procedure for total RNA extraction was performed as per the manufacturer’s instruction. Super-SAGE analysis was performed following the method of Matsumura et al. (Plos One 2010:5(8)e12010).
|
| |
|
| Data processing |
Matching of tag sequence to the C. cinerea predicted transcripts and to the genome of the strain #326 (http://genome.jgi.doe.gov/Copci_AmutBmut1 was performed with the blastn algorithm. The tag counts that matched to same gene were incremented using a script written in Perl. Fisher’s exact test of every tag count of the genes was performed by using IDEG6
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| |
|
| Submission date |
Jun 02, 2017 |
| Last update date |
Dec 03, 2018 |
| Contact name |
Yuichi Sakamoto |
| E-mail(s) |
sakamoto@ibrc.or.jp
|
| Organization name |
Iwate Biotechnology Research Center
|
| Department |
Department of Bioresource
|
| Lab |
mushroom team
|
| Street address |
Narita 22-174-4
|
| City |
Kitakami |
| State/province |
Iwate |
| ZIP/Postal code |
024-0003 |
| Country |
Japan |
| |
|
| Platform ID |
GPL23540 |
| Series (1) |
| GSE99617 |
Blue light exposure and nutrient conditions influence the expression of genes involved in simultaneous hyphal knot formation in Coprinopsis cinerea. |
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