 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 31, 2023 |
| Title |
C-S (salinity sensitive) |
| Sample type |
SRA |
| |
|
| Source name |
S-type lateral roots
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: IR29
tissue: S-type lateral roots
phenotype: salinity sensitive
|
| 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 |
same as GSM2309681
|
| 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
|
| |
|
| Submission date |
May 29, 2017 |
| Last update date |
Jan 02, 2024 |
| 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) |
| GSE99383 |
Transcriptome diversity among rice root types in salinity tolerant and sensitive varieties |
|
| Relations |
| Alternative to |
GSM2309681 |
| BioSample |
SAMN07175231 |
| SRA |
SRX2867081 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
