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| Status |
Public on Mar 30, 2017 |
| Title |
58M-71 PhyB-1 7DAP |
| Sample type |
SRA |
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| Source name |
tiller buds
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| Organism |
Sorghum bicolor |
| Characteristics |
strain: tiller bud
tissue: First leaf axil
age: 7 Days After Planting
genotype: phyB-1
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| Growth protocol |
PhyB-1 and wild-type plants were grown in the growth chamber and buds in the the first leaf axil were sampled (three biological replicates for each sample) at 6 DAP (Days After Planting), 7 DAP and 8 DAP.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted from tiller buds using TRIzol (Invitrogen)
RNA-seq libraries were prepared using the TruSeq™ RNA Sample Prep Kit v2 (Illumina, Inc.), following the recommended protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
58M-71_I21_GTTTCG_R1
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| Data processing |
The sequence reads were aligned with the sorghum transcript sequence Sbicolor-v2.1_255 version (Phytozome) using CLC Main Workbench Version 7 (CLC Inc., Aarhus, Denmark).
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.38 and RTA 1.18.61 software with default parameter settings.
RNA-seq datasets were analyzed using the Edge statistical test in the CLC Main Workbench Version 7 (CLC Inc., Aarhus, Denmark).
Supplementary_files_format_and_content: Excel file include RPKM values for each Sample …
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| Submission date |
Mar 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
John Mullet |
| Organization name |
Texas A&M University
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| Street address |
300 Olsen Boulevard
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| City |
College Station |
| ZIP/Postal code |
77843-2128 |
| Country |
USA |
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| Platform ID |
GPL21615 |
| Series (1) |
| GSE79389 |
RNA-seq Transcriptome Profiling of Tiller Buds in the First Leaf Axil of Phytochrome B mutant (phyB-1) and Wild-type Sorghum from Initiation to Dormancy (phyB-1) and Outgrowth (wild-type) |
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| Relations |
| BioSample |
SAMN04568212 |
| SRA |
SRX1642042 |
| 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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