|
| Status |
Public on Jul 20, 2022 |
| Title |
Qiagen_S1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria cell
|
| Organism |
Clostridium autoethanogenum |
| Characteristics |
strain: DSM 23693
physiological state: CO chemostat at 1 day-1
|
| Treatment protocol |
Culture was pelleted by rapid centrifugation (5,000 × g for 3 min at 4C) followed by resuspension in 5 mL of RNAlater (Qiagen). Samples were stored at 4C overnight, centrifuged (4000 × g for 10 min at 4C) and the pellets stored at -80C.
|
| Growth protocol |
Clostridium autoethanogenum was grown on syngas or CO in chemically defined medium anaerobically at 37C and a pH of 5 in chemostats at dilution rate ~1 and 2.0 day-1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen pellets were thawed and total RNA was extracted using cellular lysis in RNase-free acid-washed glass beads (Merck) and RNeasy mini kit (Qiagen) with off-column DNase treatment followed by enrichment and purification using RNA Clean & ConcentratorTM (Zymo Research).
Ribosomal RNA were removed as follows: samples referred to as “NuGEN” were processed with Prokaryotic AnyDeplete™ (0363; NuGEN), “Qiagen” samples with QIAseq® FastSelect™ Kit (335925; Qiagen), and “Zymo” samples with Zymo-Seq RiboFree™ Total RNA Library Kit (R3000; Zymo Research)
Stranded mRNA libraries were prepared for NuGEN samples with Universal Prokaryotic RNA-Seq, Prokaryotic AnyDeplete™ (0363; NuGEN); for Qiagen samples with QIAseq® Stranded RNA Lib Kit (180743; Qiagen); for Zymo with Zymo-Seq RiboFree™ Total RNA Library Kit (R3000; Zymo Research). Constructed mRNA libraries were prepared for sequencing using the MiSeq v3 150 cycles sequencing kit (MS-102-3001; Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
The quality of NextSeq raw reads was verified using MultiQC (Ewels et al., 2016) and adapter sequences were trimmed using the Cutadapt package (version 2.10; Martin 2011)
Sequencing reads were aligned and mapped to the genome of C. autoethanogenum DSM 10061 (NC_022592.1) using the Rsubread package (version 2.4.2; Liao et al., 2019).
Genomic features were assigned using the featureCounts functions within Rsubread
Raw library sizes were normalized and transcript abundances in reads per kilobase of transcript per million mapped reads (RPKM) were estimated from feature counts and gene lengths using edgeR (version 3.32.1; Robison et al., 2010).
Assembly: NC_022592.1
Supplementary files format and content: RPKM value tab-delimited text files
|
| |
|
| Submission date |
Apr 18, 2022 |
| Last update date |
Jul 20, 2022 |
| Contact name |
Kaspar Valgepea |
| E-mail(s) |
kaspar.valgepea@ut.ee
|
| Organization name |
University of Tartu
|
| Department |
Institute of Technology
|
| Street address |
Nooruse 1, room 520
|
| City |
Tartu |
| State/province |
Tartu |
| ZIP/Postal code |
50411 |
| Country |
Estonia |
| |
|
| Platform ID |
GPL32172 |
| Series (1) |
| GSE200959 |
RNA-seq sample preparation kits strongly affect transcriptome profiles of a gas-fermenting bacterium |
|
| Relations |
| BioSample |
SAMN27620091 |
| SRA |
SRX14889842 |
