|
| Status |
Public on Apr 25, 2018 |
| Title |
PB-1_Panicle_Repl1 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Panicle
|
| Organism |
Oryza sativa |
| Characteristics |
subspecies, cultivar: Genotype: Rice, Indica, Pusa Basmati 1 (PB-1)
tissue: panicle
subspecies: Indica
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from two different tissues, flagleaf and panicle of selected rice species were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adapter was removed and low quality bases were trimmed from sequenced reads.
The processed reads were aligned to the rice genome using TopHat (v2.1.1).
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: Tab delimited text files including FPKM for each sample.
|
| |
|
| Submission date |
Mar 05, 2018 |
| Last update date |
Apr 25, 2018 |
| Contact name |
Shivaprasad Padubidri V. |
| E-mail(s) |
[email protected]
|
| Phone |
+91 80 2366 6511
|
| Organization name |
National Center for Biological Sciences
|
| Department |
Plant epigenetics
|
| Street address |
GKVK Campus, Bellary road
|
| City |
Bangalore |
| ZIP/Postal code |
560065 |
| Country |
India |
| |
|
| Platform ID |
GPL21087 |
| Series (2) |
| GSE111438 |
Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [RNA-seq] |
| GSE111472 |
Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits |
|
| Relations |
| BioSample |
SAMN08637060 |
| SRA |
SRX3766117 |
