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| Status |
Public on May 01, 2020 |
| Title |
spik_stage4_r2_sRNA |
| Sample type |
SRA |
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| Source name |
sRNA Setaria viridis spikelet, stage 4 (completely out of leaf sheath)
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| Organism |
Setaria viridis |
| Characteristics |
tissue: spikelet
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| Extracted molecule |
total RNA |
| Extraction protocol |
sRNA library constructed from leaf, whole panicle, and spikelet of Setaria. The small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by Illumina TruSeq sample preparation followed by sequencing with Illumina's HiSeq 2000 instrument. The adapter sequences were removed, and the abundance of each distinct small RNA was determined.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
small RNA
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| Data processing |
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 34 nucleotides. small RNA reads were mapped to the maize genome (version JGI version1 genome).
Genome_build: Setaria Genome (version JGI version1)
Supplementary_files_format_and_content: Tag count file: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences
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| Submission date |
Apr 30, 2020 |
| Last update date |
Sep 09, 2020 |
| Contact name |
Blake C. Meyers |
| E-mail(s) |
bmeyers@danforthcenter.org
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| Phone |
314-587-1422
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| Organization name |
Donald Danforth Plant Science Center
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| Lab |
Meyers lab
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| Street address |
975 N Warson Road
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
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| Platform ID |
GPL21478 |
| Series (1) |
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| Relations |
| BioSample |
SAMN14777273 |
| SRA |
SRX8213745 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4506152_spik_stage4_r2_sRNA_chopped.txt.gz |
24.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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