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Sample GSM1385998 Query DataSets for GSM1385998
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

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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