|
| Status |
Public on Apr 27, 2015 |
| Title |
Cel2-Hyb |
| Sample type |
SRA |
| |
|
| Source name |
Clostridium cellulolyticum
|
| Organism |
Ruminiclostridium cellulolyticum |
| Characteristics |
strain: H10
carbon source: cellulose
purification: Hyb (subtractive hybridization)
|
| Growth protocol |
Clostridium cellulolyticum ATCC35319 (H10) was cultured anaerobically in 250 mL flasks with 100 mL working volume of DCB-1 medium at 35oC. Fermentation experiments included three different substrates in separate yet paralleled cultivations: (i) 3.0 g/L of glucose and (ii) 3.0 g/L of cellobiose, and (iii) 5g/L of cellulose. A 1% (v/v) inoculum of culture pre-adapted on various substrates in vials was used for inoculation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cultures harvested at the mid-log phase using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. Genomic DNA was removed by RNase-Free DNase Set (Qiagen).Two strategies were applied for purification of mRNA from total RNA. One is to remove 16S and 23S rRNA from total RNA using MicrobExpressTM Bacterial mRNA Purification kit (Ambion) (named Hyb). The other is depletion of rRNA of total RNA using Terminator TM 5’-phosphate-dependent exonuclease (TEX) (Epicentre #TER51020).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 10
|
| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to H10 whole genome using SOAP 2.20 with parameters -m 100 -x 1000 -n 5 -v 2 -p 30
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: H10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
May 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Xu |
| E-mail(s) |
xujian@qibebt.ac.cn
|
| Organization name |
Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences
|
| Lab |
Jian lab
|
| Street address |
No.189 Songling Road, Laoshan District
|
| City |
Qingdao |
| State/province |
Shandong |
| ZIP/Postal code |
266101 |
| Country |
China |
| |
|
| Platform ID |
GPL18692 |
| Series (1) |
| GSE57652 |
Genome-wide maps of primary and processed start-sites of transcripts revealed mechanism controlling in vivo stoichiometry of protein complex in bacteria |
|
| Relations |
| BioSample |
SAMN02777122 |
| SRA |
SRX542115 |
