|
| Status |
Public on Sep 23, 2021 |
| Title |
S-L |
| Sample type |
SRA |
| |
|
| Source name |
L-type lateral roots
|
| Organism |
Oryza sativa |
| Characteristics |
genotype: IR29
treatment: Salt
|
| Treatment protocol |
Control and salt treatment (50 mM NaCl) for 7 days
|
| Growth protocol |
Growth condition: at 30°C/25°C, humidity of 70%/75% (day12h/night12h)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from root tissues using RNeasy Plant Mini Kit (QIAGEN).
strand-specific mRNA-seq library (insert size 200 bp)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
S_L
|
| Data processing |
Adaptor sequences and low-quality reads/nucleotides were removed using trimmomatic (ver. 0.32).
Cleaned reads were used for mapping on reference sequence using bowtie (ver. 2-2.2.2) and tophat (ver. 2.0.11).
Assembly of transcripts and the calculation of the expression level were done using cufflinks (ver. 2.2.1).
Transcripts of all the samples obtained using cufflinks were assembled using cuffmerge (ver. 2.2.1).
Using cuffdiff (ver. 2.2.1), the expression level was compared among samples using the transcripts information obtained from the cuffmerge analysis.
Genome_build: IRGSP-1.0_genome.fa
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
Supplementary_files_format_and_content: COUNT_TRACKING File
Supplementary_files_format_and_content: FPKM_TRACKING File
Supplementary_files_format_and_content: diff
|
| |
|
| Submission date |
Sep 13, 2016 |
| Last update date |
Sep 24, 2021 |
| Contact name |
Joyce Cartagena |
| Organization name |
Nagoya University
|
| Street address |
Furo-cho, Chikusa-ku
|
| City |
Nagoya |
| ZIP/Postal code |
464-8601 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19290 |
| Series (1) |
| GSE86860 |
Comparative transcriptome analysis of different root types of a salinity sensitive rice cultivar under salinity stress |
|
| Relations |
| BioSample |
SAMN05768177 |
| SRA |
SRX2161892 |
