|
Status |
Public on Jul 08, 2014 |
Title |
∆vib-1 Avicel #1 |
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 Genome Analyzer IIx |
|
|
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 |
GPL17918 |
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 |
SAMN02401847 |
SRA |
SRX376838 |