|
| Status |
Public on Sep 01, 2013 |
| Title |
Nc WT Avicel #2 |
| Sample type |
SRA |
| |
|
| Source name |
hyphae
|
| Organism |
Neurospora crassa OR74A |
| Characteristics |
genotype: wildtype
carbon source: Avicel
|
| Growth protocol |
N. crassa strains were innoculated in 100mL Liquid media with 2% sucrose, grown 16 hours at 25C 200rpm and constant light. Mycelia were washed once in media with no carbon sourse and resuspended in fresh media with 2% Avicel PH-101, 2% sucrose or no added carbon source, then grown and additional 4hrs at 25C. A. nidulans strains were innuculated in 100mL Liquid media with 1% glucose, grown 16 hours at 37C 200rpm and constant light. Mycelia were washed once in media with no carbon sourse and resuspended in fresh media with 2% Avicel PH-101 or no added carbon source, then grown and additional 6hrs at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelia were harvested by filtration and flash frozen in liquid nitrogen. RNA was extracted by bead-beating in TRIZOL reagent and purified with Rneasy columns 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 |
| |
|
| Description |
multiplexed: no
|
| Data processing |
Illumina CASAVA_v1.8.0 software used for basecalling.
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 --compatible-hits-norm --max-bundle-frags=10000000)
Rawcounts were calculated with Htseq Count (options: -m intersection-strict --stranded=no)
Differential Expression was estimated with DESeq (method="per-condition")
Genome_build: N. crassa: OR74A version 10 from the Broad Institute.
Genome_build: A. nidulans: FGSC A4 version s09-m01-r04 from the Aspergillus Genome Database (AspGD.org)
Supplementary_files_format_and_content: .fpkm_tracking: tab-delimited output from cufflinks
Supplementary_files_format_and_content: .txt: tab-delimied output from DEseq
Supplementary_files_format_and_content: 2489_DESeq_AvN.txt: differential expression analysis for FGSC 2489 on Avicel versus No Carbon media
Supplementary_files_format_and_content: A4_DESeq_AvN.txt: differential expression analysis for FGSC A4 on Avicel versus No Carbon media
|
| |
|
| Submission date |
Feb 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
N Louise Glass |
| Organization name |
UC Berkeley
|
| Department |
Plant and Microbial Biology
|
| Lab |
Glass Lab
|
| Street address |
341 Koshland Hall, Univerisity of California
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720-3102 |
| Country |
USA |
| |
|
| Platform ID |
GPL15146 |
| Series (1) |
| GSE44100 |
Inducer Free Cellulase Secretion in Neurospora Crassa and comparitive analysis of cellulase induction in Aspergillus nidulans |
|
| Relations |
| SRA |
SRX226239 |
| BioSample |
SAMN01914758 |
