|
| Status |
Public on May 01, 2015 |
| Title |
PXO99A with dTal280 replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
leaf tissue
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Nipponbare
tissue: leaf
pathogen: Xanthomonas oryzae pv. oryzae strain PXO99A with dTal280
|
| Treatment protocol |
Plants were inoculated at four weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.9 by infiltration using a needleless syringe. A region from the leaf tip to about 5 cm from the tip was completely infiltrated with contiguous spots. Tissue was collected individually from each leaf after 48 hours.
|
| Growth protocol |
Oryza sativa L. ssp. japonica cv. Nipponbare plants to be inoculated were grown in LC-1 soil mixture (Sungro, Bellevue, WA) in PGC15 growth chambers (Percival Scientific, Perry, IA) in trays approximately 60 cm below a combination of fluorescent and incandescent bulbs providing approximately 1,000 μmoles/m2/s measured at 15 cm, under a cycle of 12 h of light at 28 °C and 12 h of dark at 25 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the Qiagen RNeasy kit and manufacturer's protocol.
These libraries were prepped with the Illumina TruSeq RNA Sample Prep v2 kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Adapters were trimmed using the Trimmomatic v0.22 ILLUMINACLIP function (Bolger et al., 2014) for single end reads with seedMismatches=2, palindromeClipThreshold=30, and simpleClipThreshold=7
Low quality bases at the ends of reads were trimmed using BRAT trim v2.0.1 (Harris et al., 2010) with the parameters "-q 20 -L 33"
Reads were aligned using Tophat v2.06 with command line options '--num-threads 8 --max-intron-length 10000' and with the -G option specifying that the the MSU Release 7.0 annotation downloaded from the Rice Genome Annotation Project be used to guide transcript assembly
The number of reads aligned to each gene was determined using HTSeq-count (Anders et al., 2014) from the HTSeq framework version 0.5.4p3 with the command line options ‘-i ID -t gene -s no’
Genome_build: The Oryza sativa L. ssp. japonica (cv. Nipponbare) reference genome v.7.0 was downloaded from Phytozyme 10
Supplementary_files_format_and_content: the processed files are text tab-delimited files output by HTSeq-count with locus IDs in the first column and the number of reads aligned to each locus in the second column. The last five lines in each file don't include reads aligned to specific loci, but the number of reads in the following categories: those aligned to no annotated feature (no_feature), those that cannot be unambiguously assigend to a single feature (ambiguous), reads with an alignment quality lower than ten (too_low_aQual), reads that are not aligned (not_aligned), and reads that are aligned to multiple locations (alignment_not_unique)
|
| |
|
| Submission date |
Apr 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Adam Bogdanove |
| E-mail(s) |
boglab@gmail.com
|
| Phone |
(607) 255-7831
|
| Organization name |
Cornell University
|
| Department |
Plant Pathology and Plant-Microbe Biology
|
| Lab |
Bogdanove Lab
|
| Street address |
334 Plant Science Building
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL13834 |
| Series (1) |
| GSE67958 |
Host transcriptional reprogramming in response to the rice bacterial blight pathogen Xanthomonas oryzae pv.oryzae constitutively expressing the X. oryzae pv. oryzicola TAL2a effector from the high copy vector pKEB31 |
|
| Relations |
| BioSample |
SAMN03487371 |
| SRA |
SRX997482 |
