|
| Status |
Public on Sep 01, 2015 |
| Title |
2489_4X_Vogels2 |
| Sample type |
SRA |
| |
|
| Source name |
whole fungus
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: Neurospora crassa OR74A (FGSC2489)
genotype: Neurospora crassa OR74A (FGSC2489)
|
| Treatment protocol |
The filamentous fungus was washed and transferred to fresh Vogel's Media with Xylan or Sucrose as the carbon source or Vogel's without a carbon source.
|
| Growth protocol |
Neurospora crassa was grown on Vogel's Mininal Media for 16 hrs with Sucrose as the carbon source
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Phenol Chlorophorm, ethanol precipitated, and DNAsed and cleaned on a Qiagen column
Libraries were prepared using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
alignment was performed by Tophat (v2.04)
Raw Gene counts was performed by Htseq (0.6)
Gene counts were normalized by Cufflinks (v2.02)
Differential expression was performed with Cuffdiff (v2.02)
Genome_build: aligned to Neurospora crassa genome version 12 mitochondria version 10 (BROAD)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values, raw gene counts, and differential expression analysis comparing 2 or more libraries
|
| |
|
| Submission date |
May 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
James Craig |
| E-mail(s) |
jimcraig134@gmail.com
|
| Organization name |
UC Berkeley
|
| Department |
Plant & Microbial Biology
|
| Lab |
N. Louise Glass
|
| Street address |
341A Koshland Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL16164 |
| Series (2) |
| GSE68514 |
Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1 (RNA-Seq) |
| GSE68517 |
Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1 |
|
| Relations |
| BioSample |
SAMN03581137 |
| SRA |
SRX1017001 |
