|
| Status |
Public on Dec 14, 2019 |
| Title |
ntj2_mock_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
mock-inoculated sorghum leaves
|
| Organism |
Sorghum bicolor |
| Characteristics |
sorghum genotype: ntj2
treatment: sorghum mock inoculation
tissue: mock-inoculated sorghum leaves
time point: 48 hours post inoculation
|
| Treatment protocol |
The fourth leaf of sorghum plants was inoculated with 10mM MgCl2 and bacterial suspensions as the mock and Xvh-inoculated treatments, respectively. Bacteria were harvested from the plates containing NYGA medium as “Xvh-culture” samples.
|
| Growth protocol |
The sroghum plants were grown in a growth chamber set at 28/23°C with 14/10 h (day/night) conditions and 50% relative humidity. 14-day-old plants were used for all experiments. Bacterial strain were grown on plates containing NYGA medium (per liter: 5.0g peptone, 3.0g yeast extract, 20.0g glycerol, and 1% agar) for 48 hours at 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol™ Reagent (Invitrogen). The aqueous phase containing the RNA was mixed with an equal volume of 70% ethanol, and then applied to a column from the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich) following the manufacturer’s instructions, including the On-Column DNase Digestion protocol. RNA quality was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were trimmed with Trimmomatic. HISAT2 (version 2.0.6) was used to align the RNA-seq reads against a concatenated genome comprised of the sorghum nuclear genome (version Sorghum bicolor v3.1.1; https://phytozome.jgi.doe.gov), the sorghum chloroplast genome (GenBank: EF115542.1), the sorghum mitochondrial genome (NCBI Reference Sequence: NC_008360.1), and the Xvh genome (https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2757320517) to allow for the best alignment of each read. Default parameters were used except for the inclusion of the '--dta-cufflinks' parameter. The resulting SAM (Sequence Alignment/Map) files (.sam) were sorted and converted to BAM (Binary Alignment/Map) files (.bam) using SAMtools.
Stringtie was used for quantification. The parameter -e was used to limit quantification to alignments matching the reference annotation file (parameter -G). Transcripts were then merged with Stringtie Merge. Both stringtie steps were done with -G parameter using either sorghum or xanh annotation file. This was performed twice, once to quantify the reads mapped to the sorghum genome and again to quantify the reads mapped to the Xvh genome
The Ballgown FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were calculated by Stringtie with the -b parameter, using merged transcripts from stringtie merge as -G parameter.
Genome_build: Sorghum nuclear genome (version Sorghum bicolor v3.1.1; https://phytozome.jgi.doe.gov), the sorghum chloroplast genome (GenBank: EF115542.1), the sorghum mitochondrial genome (NCBI Reference Sequence: NC_008360.1), and the Xanthomonas vasicola pv. holcicola BLS185 genome (https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2757320517)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Dec 13, 2019 |
| Last update date |
Dec 16, 2019 |
| Contact name |
Rebecca Bart |
| E-mail(s) |
[email protected]
|
| Phone |
314-587-1696
|
| Organization name |
Donald Danforth Plant Science Center
|
| Lab |
Bart Lab
|
| Street address |
975 North Warson Road
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL27913 |
| Series (1) |
| GSE142035 |
Escalation in the host-pathogen arms race: a host resistance response corresponds to a heightened bacterial virulence response |
|
| Relations |
| BioSample |
SAMN13561714 |
| SRA |
SRX7368483 |
