|
| Status |
Public on Jul 08, 2014 |
| Title |
∆vib-1 Avicel #3 |
| Sample type |
SRA |
| |
|
| Source name |
mycelia
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: FGSC 11308
genotype: ∆vib-1 a
treatment: Avicel
|
| Growth protocol |
N. crassa strains were innoculated in 100mL Liquid media with 2% sucrose, grown 16 hours at 25ºC 200rpm and constant light. Mycelia were washed once in media with no carbon sourse and resuspended in fresh media with 2% Avicel PH-10 or without carbon sources, then grown an additional 4hrs at 25ºC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelia were harvested by filtration and flash frozen in liquid nitrogen. Total RNA was extracted by bead-beating in TRIZOL reagent and purified with RNeasy kit from Qiagen.
mRNA was enriched with oligo-dT magnetic beads, fragmented and reverse transcribed with Superscript II reverse polymerase from Invitrogen. Illumina adapters were added to the cDNA library with the TruSeq DNA kit v2, SetA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalling performed using Illumina CASAVA_v1.8.0 software
Reads were mapped to known transcripts with Tophat v2.0.4 (options: --GTF)
Fragments Per exon Kilobase per Megabase read (FPKM) were calculated with Cufflinks v2.0.2 (options: -u -b -G --max-bundle-frags=10000000)
Differential Expression was estimated with Cuffdiff v2.0.2 (options: -u -b -G --max-bundle-frags=10000000)
Genome_build: N. crassa: OR74A version 10 from the Broad Institute
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Nov 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
N. Louise Glass |
| E-mail(s) |
lglass@berkeley.edu
|
| Organization name |
UC Berkeley
|
| Department |
Plant and Microbial Biology
|
| Lab |
Glass
|
| Street address |
341 Koshland Hall, Univerisity of California
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720-3102 |
| Country |
USA |
| |
|
| Platform ID |
GPL16164 |
| Series (1) |
| GSE52316 |
VIB1, a link between glucose signaling and carbon catabolite repression, is essential for plant cell wall degradation by Neurospora crassa |
|
| Relations |
| BioSample |
SAMN02401852 |
| SRA |
SRX376840 |
