|
| Status |
Public on Mar 01, 2018 |
| Title |
Glucose 1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole organism, glucose
|
| Organism |
Trametes cinnabarina |
| Characteristics |
strain/background: PB94
tissue: Whole organism
energy substrate: Glucose
|
| Treatment protocol |
Fungal cultures were grown on glucose, maltose, cellobiose, poplar, switchgrass, or no energy substrate (control).
|
| Growth protocol |
Cultures were grown on semi-minimal media and inoculated with a 5mm agar cube overgrown with P. cinnabarinus. Cultures were grown for at least 5 days before harvesting RNA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Mini Kit (Plant/Fungi Protocol).
Illumina TruSeq Stranded mRNA library standard protocol for Soluble substrate and control, Ribozero (yeast) kit used to remove rRNA from Poplar and Switchgrass samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
mRNA
Processed data file: pyc_expressiondata_expectedcounts.txt
Processed data file: pyc_substrate_tpm.txt
|
| Data processing |
Assembled transcriptome using reads obtained from growth on each substrate and the Trinity algorithm.
Aligned reads from all conditions to transcriptome to get count data.
Genome_build: de novo
Supplementary_files_format_and_content: pyc_expressiondata_expectedcounts.txt: Tab-delimited text file contains the expected counts produced by RSEM analysis.
Supplementary_files_format_and_content: pyc_substrate_tpm.txt: Tab-delimited text file contains the transcripts per million counts produced by the RSEM analysis.
Supplementary_files_format_and_content: Pycnoporus_denovo.fasta: FASTA file contains all transcripts assembled by Trinity; de novo transcript assembly.
|
| |
|
| Submission date |
Jul 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
John Henske |
| E-mail(s) |
johnhenske@engineering.ucsb.edu
|
| Organization name |
University of California, Santa Barbara
|
| Department |
Department of Chemical Engineering
|
| Street address |
Engineering II Building
|
| City |
Santa Barbara |
| State/province |
CA |
| ZIP/Postal code |
93106-5080 |
| Country |
USA |
| |
|
| Platform ID |
GPL23829 |
| Series (1) |
| GSE101869 |
Substrate-based regulation in Pycnoporus cinnabarinus PB94 |
|
| Relations |
| BioSample |
SAMN07414160 |
| SRA |
SRX3033989 |
