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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 02, 2020 |
| Title |
sRNA Shoot |
| Sample type |
SRA |
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| Source name |
shoot
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| Organism |
Asparagus officinalis |
| Characteristics |
tissue: shoot
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol RNA
The small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by Illumina sRNA TruSeq sample preparation kit followed by sequencing with Illumina's HiSeq 2500 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 2500 |
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| Description |
St_Aspa
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.
Genome_build: Asparagus officinalis v1.1 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Aofficinalis_er)
Supplementary_files_format_and_content: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences
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| Submission date |
May 01, 2020 |
| Last update date |
May 07, 2020 |
| Contact name |
Alex Harkess |
| E-mail(s) |
aharkess@hudsonalpha.org
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| Organization name |
HudsonAlpha Institute for Biotechnology
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| Street address |
601 Genome Way
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| City |
Huntsville |
| State/province |
AL |
| ZIP/Postal code |
35806 |
| Country |
USA |
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| Platform ID |
GPL24857 |
| Series (1) |
| GSE149730 |
The asparagus genome sheds light on the origin and evolution of a young Y chromosome |
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| Relations |
| BioSample |
SAMN14791560 |
| SRA |
SRX8241480 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4509845_3403_tag_count.txt.gz |
97.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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