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| Status |
Public on Jan 31, 2021 |
| Title |
OE_seedling_Rep2 |
| Sample type |
SRA |
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| Source name |
Five weeks old seedlings
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| Organism |
Oryza sativa |
| Characteristics |
subspecies, cultivar: Genotype: Rice, Indica, Pusa Basmati 1 (PB1)
transgenic line: OE
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 5 week old seedlings of both wild-type and transgenic knock-down lines were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Adapter was removed and low quality bases were trimmed from sequenced reads.
The processed reads were aligned to the rice genome, Oryza sativa Indica
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Supplementary_files_format_and_content: FPKM values of the genes obtained using Cuffdiff are provided as tsv format
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| Submission date |
May 29, 2018 |
| Last update date |
Jan 31, 2021 |
| Contact name |
Shivaprasad Padubidri V. |
| E-mail(s) |
shivaprasad@ncbs.res.in
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| Phone |
+918023666511
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| Organization name |
National Centre for Biological Sciences, TIFR
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| Street address |
GKVK Campus, Bellary Road
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| City |
Bengaluru |
| State/province |
Karnataka |
| ZIP/Postal code |
560065 |
| Country |
India |
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| Platform ID |
GPL23013 |
| Series (1) |
| GSE115053 |
RNA-seq datasets of OsRDR3 transgenic plants. |
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| Relations |
| BioSample |
SAMN09278058 |
| SRA |
SRX4137896 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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