|
| Status |
Public on Oct 01, 2017 |
| Title |
S4 Avicel 1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole organism
|
| Organism |
Anaeromyces robustus |
| Characteristics |
energy substrate: Avicel
growth phase harvested from: Exponential growth
|
| Treatment protocol |
See characteristics for energy source treatments
|
| Growth protocol |
Cultures grown in ~ 10 ml Medium C (Davies et. al, J Gen Microbiol. 1993 Jun;139 Pt 6:1395-400.) at 39°C to mid-log phase (P≥5 psi)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNEasy Mini Kit (Plant/Fungi Protocol)
Illumina TruSeq Stranded mRNA library standard protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
S4_substrate_raw_tpm.txt
S4_substrate_raw_expectedcounts.txt
A1
|
| Data processing |
Aligned reads from all conditions to transcriptomes using Trinity utility align_and_estimate_abundance.pl with RSEM estimation method
Genome_build: de novo
Supplementary_files_format_and_content: tab delimited text files containing estimated abundances of each transcript
|
| |
|
| Submission date |
Feb 28, 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 |
GPL23124 |
| Series (1) |
| GSE95479 |
Substrate-based regulation in gut fungi |
|
| Relations |
| BioSample |
SAMN06468428 |
| SRA |
SRX2598489 |
