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| Status |
Public on Aug 20, 2021 |
| Title |
Roots |
| Sample type |
SRA |
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| Source name |
Roots
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| Organism |
Aegilops tauschii |
| Characteristics |
cultivar: AL8/78
tissue: Roots
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| Treatment protocol |
None
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| Growth protocol |
Seeds of Ae. tauschii accessions were germinated in dark, grown, and corresponding materials were collected
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from roots, spikes, mature leaves, and seedlings of AL8/78 using TriReagent (Millpore-Sigma, St. Louis, USA) following manufacturer’s protocols
Libraries were generated using 20 ng of RNA after size selection on polyacrylamide gels, and using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, USA)
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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 |
A_tauschii_Roots_S2
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| Data processing |
Briefly, library quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Adapters were trimmed using Trimmomatic v0.32 (PMID: 24695404) with a minimum and maximum length of 18 nt and 34 nt
Mapped to the new genome wa done with Bowtie2
miRNA and phasiRNA predictions were done using both ShortStack (PMID: 27175019) and miR-PREFeR (PMID: 24930140) and filtering criteria recommended in Axtell and Meyers (PMID: 29343505)
Genome_build: Ae. tauschii acc. AL8/78 reference genome sequence v. 5 (an updated version of the assembly (Aet v4.0) under the BioProject PRJNA341983)
Supplementary_files_format_and_content: Count file containing sequence and abundance
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| Submission date |
Mar 18, 2021 |
| Last update date |
Aug 20, 2021 |
| Contact name |
Patricia Baldrich Gonzalez |
| E-mail(s) |
[email protected]
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| Organization name |
University of California - Davis
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| Department |
Genome Center
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| Lab |
Meyers Lab
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| Street address |
451 Health Sciences Dr., Davis, CA 95616
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL26494 |
| Series (1) |
| GSE169198 |
Aegilops tauschii reference genome sequence Aet v5.0 including annotation of small RNAs and reannotation of protein-coding genes |
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| Relations |
| BioSample |
SAMN18353233 |
| SRA |
SRX10381498 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5182811_8442_chopped.txt.gz |
55.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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