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| Status |
Public on Nov 19, 2019 |
| Title |
no MuDR no Muk rep1 |
| Sample type |
SRA |
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| Source name |
Leaf 2
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| Organism |
Zea mays |
| Characteristics |
tissue: Leaf
genotype: tester control (IT)
Stage: Young leaf 2
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| Growth protocol |
greenhouse with a 12 hour light cycle
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using an SDS-based extraction solution and precipitated using ethanol. The pellet was dissolved in water, heated to 65°C for 5 min, and then placed on ice. Polyethylene glycol (molecular weight 8000; Sigma) was added to a final concentration of 5% and NaCl to a final concentration of 0.5 M. After an 1 hour incubation on ice, the RNA was centrifuged at 10,000g for 10 min. Three volumes of ethanol were added to the supernatant, and the RNA was precipitated at –20°C for at least 2 hrs. The low molecular weight RNAs were pelleted by centrifugation for 10 min at 10,000g. Small RNAs were detected in Polyacrylamide gel electrophoresis (PAGE) gel and purified by ZR small-RNA™ PAGE Recovery Kit.
Small RNA library was prepared by ScriptMiner™ Small RNA-Seq Library Preparation Kit for Ilumina sequencing.
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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 |
total small RNA
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| Data processing |
Base-calling
The small RNA sequencing data from different libraries was trimmed and filtered for low quality reads, adapter sequences, and reads matching structural noncoding RNAs (t/r/sn/snoRNAs) collected from Rfam (http://rfam.sanger.ac.uk). The kept reads with a length of 18-26 nt were mapped to MuDR(p1) and Muk, and their flanking 500 bp upstream and downstream sequences using Bowtie only allowing perfect matches.
Small RNA abundance was normalized to reads per million.
The data was viewed using Intergrative Genomics Viewer. Small RNAs for the mop1 and lbl1 mutants were downloaded from previous studies, trimmed and mapped to MuDR sequences.
Genome_build: MuDR (M76978.1) and Muk (DQ011286.1)
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample
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| Submission date |
Sep 13, 2017 |
| Last update date |
Nov 19, 2019 |
| Contact name |
Meixia Zhao |
| E-mail(s) |
xiami1119@163.com
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| Organization name |
Purdue University
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| Department |
Agronomy
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| Street address |
915 W State Steet
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| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platform ID |
GPL15463 |
| Series (1) |
| GSE103833 |
Silencing of Mu elements in maize involves distinct populations of small RNAs and distinct patterns of DNA methylation |
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| Relations |
| BioSample |
SAMN07638813 |
| SRA |
SRX3182985 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2782566_HL_03A_index3_TTAGGC_L003_R1_TPM.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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