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Sample GSM2514967 Query DataSets for GSM2514967
Status Public on Oct 01, 2017
Title S4 Switchgrass 1
Sample type SRA
 
Source name Whole organism
Organism Anaeromyces robustus
Characteristics energy substrate: Switchgrass
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
SG1
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 SAMN06468422
SRA SRX2598495

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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