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| Status |
Public on Aug 03, 2018 |
| Title |
MIMall_2 |
| Sample type |
SRA |
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| Source name |
Medicago hairy roots
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| Organism |
Medicago truncatula |
| Characteristics |
ecotype: Jemalong A17
tissue: hairy roots
genotype/variation: target mimics for miR1507, miR2109, and miR2118a/b/c
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| Extracted molecule |
total RNA |
| Extraction protocol |
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Plant RNA reagent (Ambion, Life Technologies, USA) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001). PARE libraries were constructed according to the protocols by German et al., 2009 and Zhai et al., 2014.
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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
Medicago target mimics for miR1507, miR2109, and miR2118a/b/c rep 2
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| Data processing |
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: Medicago Genome v3.5
Supplementary_files_format_and_content: tag count file
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| Submission date |
Aug 03, 2018 |
| Last update date |
Aug 07, 2018 |
| Contact name |
Blake C. Meyers |
| E-mail(s) |
[email protected]
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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 |
GPL17491 |
| Series (1) |
| GSE67613 |
Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances |
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| Relations |
| BioSample |
SAMN09765271 |
| SRA |
SRX4506857 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3318747_MIMall_2_chopped.txt.gz |
42.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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