|
| Status |
Public on Nov 30, 2018 |
| Title |
dim5_DD_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mycelia
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: dim5
harvest time: DD24
|
| Treatment protocol |
For DD24 cultures were grown in the light for 24 hours then transferred to constant dark for 24 hours and harvested. The LP30 were grown in a similar fashion but just prior to harvesting the cultures were placed in constant light for 30 min prior to harvesting. The tissue was immediately snap frozen.
|
| Growth protocol |
For the growth, Neurospora conidia were inoculated in 2% liquid culture media (2% LCM) and grown in 100-mm Petri dishes overnight at 30 °C to generate mycelia mats. Plugs were cut from the mycelia and used to inoculate flasks containing 100 ml of 2% LCM and grown for a total of 2 days at 25 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen) following manufacturer’s instructions. The total RNA was sent to the Columbia Genome Center for library preparation and RNA-seq.
Ribosomal RNAs were depleted and the remaining RNA was for cDNA library preparation using the TrueSeq library preparation kit version 2. A total of 60 million 100bp paired-ended reads were sequenced on the Illumina 2500 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
HISAT2 (version 2.1.0) and StringTie( version 1.3.3b) for mapping and transcripts discovery. The 100bp pair-end reads were mapped to the Neurospora NC12 reference genome using the existing GTF file as a guide. The Neurospora transcriptome created by Hisat2 was assembled and merged using StringTie to generate the merged GTF file. Next, we used Cuffdiff for differential expression analysis.
Genome_build: NC12
|
| |
|
| Submission date |
Oct 16, 2018 |
| Last update date |
Nov 30, 2018 |
| Contact name |
William J. Belden |
| E-mail(s) |
beldenwj@scarletmail.rutgers.edu
|
| Phone |
848-932-5617
|
| Organization name |
Rutgers, The State University of New Jersey
|
| Department |
Animal Sciences
|
| Lab |
Belden Lab
|
| Street address |
59 Dudley Rd
|
| City |
New Brunswick |
| State/province |
NJ |
| ZIP/Postal code |
08091 |
| Country |
USA |
| |
|
| Platform ID |
GPL20705 |
| Series (2) |
| GSE121353 |
Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci [RNA-seq] |
| GSE121356 |
Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci |
|
| Relations |
| BioSample |
SAMN10248045 |
| SRA |
SRX4893759 |
