|
| Status |
Public on Oct 28, 2015 |
| Title |
SE_8-TEX |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Bacillus velezensis FZB42 |
| Characteristics |
treatment: no TEX treament
medium supplements: soil extract (SE)
growth stage: middle stationary phase (#8)
|
| Growth protocol |
B. amyloliquefaciens FZB42 was grown in 1CM media supplemented with maize root exudates (RE), or soil extract (SE), or both (RS) and sampled from different growth stage (#3 and #8).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The bacterial cells were quick-frozen in liquid nitrogen before total RNA preparation. RNAs were isolated with Trizol® agent and glass beading on FastPrep®-24 system.
Libraries for Illumina sequencing (HiSeq) of cDNA were constructed by vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/), as described previously for eukaryotic microRNA (Berezikov et al., 2006) but omitting the RNA size-fractionation step prior to cDNA synthesis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Demultiplexing
Fastq quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (via READemption)
Read mapping using segemehl (vi READemption)
Coverage calculation and normalisation (via READemption)
Genome_build: NC_009725.1
Supplementary_files_format_and_content: wiggle
|
| |
|
| Submission date |
Mar 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Li |
| Organization name |
University of California, Irvine
|
| Street address |
University of California, Irvine
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL19866 |
| Series (1) |
| GSE66681 |
Differential RNA-seq of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42 Reveals sRNA Bas01 involved in Sporulation and Biofilm Formation |
|
| Relations |
| BioSample |
SAMN03394968 |
| SRA |
SRX913699 |
