|
| Status |
Public on Mar 28, 2013 |
| Title |
Wild Louisiana N. crassa isolate 4452 |
| Sample type |
SRA |
| |
|
| Source name |
Mycelia
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: 4452
source: mycelia
age: 16 hours
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mycelia were harvested, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to FGSC 2489 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods. 2008. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the transcript and by the size of the library.
Genome_build: V10
Supplementary_files_format_and_content: tab-delimited text file including gene specific RPKM values for each Sample
|
| |
|
| Submission date |
Mar 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Robert Hall |
| E-mail(s) |
neurosporacrassa@gmail.com
|
| Phone |
510-643-2546
|
| Organization name |
UC Berkeley
|
| Department |
Plant and Microbial Biology
|
| Lab |
N. Louise Glass
|
| Street address |
341 Koshland Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL15629 |
| Series (1) |
| GSE45406 |
Genome Wide Association identifies Novel Loci Involved Fungal Communication |
|
| Relations |
| SRA |
SRX255789 |
| BioSample |
SAMN01992829 |
