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| Status |
Public on Jan 15, 2018 |
| Title |
ago18(2)_seedling_Rep-1 |
| Sample type |
SRA |
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| Source name |
Four weeks old seedlings
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| Organism |
Oryza sativa |
| Characteristics |
subspecies, cultivar: Rice, Indica, Pusa Basmati 1 (PB1)
tissue: Four weeks old seedlings
genotype: ago18
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from three different tissues, 4week old seedlings, young panicle and mature panicle 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 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: Text delimited files including FPKM for each sample.
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| Submission date |
Dec 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shivaprasad Padubidri V. |
| E-mail(s) |
shivaprasad@ncbs.res.in
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| Phone |
+91 80 2366 6511
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| Organization name |
National Center for Biological Sciences
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| Department |
Plant epigenetics
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| Street address |
GKVK Campus, Bellary road
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| City |
Bangalore |
| ZIP/Postal code |
560065 |
| Country |
India |
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| Platform ID |
GPL23013 |
| Series (1) |
| GSE107903 |
Oryza sativa Argonaute 18 is a regulator of male sterility (RNA-Seq) |
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| Relations |
| BioSample |
SAMN08160001 |
| SRA |
SRX3461198 |
| 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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