|
| Status |
Public on Nov 01, 2014 |
| Title |
SQR9_root exudates_48 h |
| Sample type |
SRA |
| |
|
| Source name |
SQR9_root exudates_48 h
|
| Organism |
Bacillus amyloliquefaciens |
| Characteristics |
strain: SQR9
incubation time: 48 h
treatment: addition of maize root exudates
|
| Treatment protocol |
Addition of the concentrated maize root exudates into the wells, control wells were treated with water
|
| Growth protocol |
Incubated at 37°C in 48-well microtiter plates filled with 1/2 MSgg medium, without shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by E.Z.N.A. @ Bacterial RNA Kit (OMEGA, bio-tek, USA), mRNA was depleted using a Ribo-ZeroTM rRNA Removal kit (Epicenter, USA), cDNA was synthesised by Superscript II reverse transcriptase (Invitrogen, America).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
7-17.txt
|
| Data processing |
clean reads obtained from the Illumina sequencing data (at least half of the bases with a quality > 5, not including N)
mapped to the B. amyloliquefaciens SQR9 genome using bowtie2 with paramenters --phred64 -x 9 --very-fast --ff -1
Collected reads from different samples of each gene were transformed into RPM (Reads Per Kilo bases per Million reads) values (Mortazavi, et al., 2008).
Genes exhibiting statistically significant expression changes between the control and treatment conditions were identified using MARS model from the DEGseq program package using the false discovery rate (FDR) control method
Only genes that met the following filter conditions were regarded as significantly expressed between control and treatment: (i) fold-change>=1.5; (ii) q-value<=0.001
Genome_build: CP006890
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Feb 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Dongqing Yang |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanjing Agricultural University
|
| Street address |
Weigang 1#, Xuanwu district
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL18285 |
| Series (1) |
| GSE54987 |
Transcriptomics of Bacillus amyloliquefaciens SQR9 to maize root exudates |
|
| Relations |
| BioSample |
SAMN02641448 |
| SRA |
SRX470265 |
