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| Status |
Public on Sep 08, 2022 |
| Title |
SGA_53h1 |
| Sample type |
SRA |
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| Source name |
seed
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| Organism |
Zea mays |
| Characteristics |
tissue: seeds
treat: different treatments of seeds
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| Treatment protocol |
The seeds were harvested at the same developmental stage (mature stage, black layer formed). Then these seeds with consistent physiological state were selected and surface-sterilized with 75% ethanol. The seeds of Yu537A were pretreated with 400mg/L gibberellin (GA3) for its lower seed vigor. Two inbred lines were germinated on the two layers of filter paper with the moisture in sterile petri dishes (the diameter was about 12 cm). The seeds were incubated at a constant temperature of 25℃ under a 14/10 h (light/dark) photoperiod with photosynthetically active radiation of 25 μmol photons m−2 s−1.
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| Growth protocol |
Two maize inbred lines, Yu82 and Yu537A were selected and used in this study. These two inbred lines were derived from Yuzong5, which is an improved population cultivar and is cultivated widely in China.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The embryos of five individual seeds were dissected with a sterile knife in each sample and then the samples were immediately frozen in liquid nitrogen and stored at −80 °C.Total RNA was extracted using RNAprep Pure Plant Kit (Tiangen) following the procedure of the manufacturer. The concentration was measured by Nanodrop 2000 and integrity of total RNA was tested on 1.0% agarose gel.
Small RNA library construction was conducted with TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). Small RNA libraries were sequenced with Illumina Hiseq2000/2500 and the sequencing read length is single-ended 1×50bp.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The program ACGT101-miR (LC Sciences, Houston, Texas, USA) used for raw data analysis of miRNAs sequencing was independently developed.
The main steps are below: removal of 3′ adaptor and junk sequences to obtain clean sequences;
screening of miRNA length of 18-25nt; compared the sequencing data to other database, including Rfam and Repbase; Rfam is a family database of non-coding Rnas (Ncrnas), including rRNA, tRNA, snoRNA, snRNA, miRNA and other non-coding Rnas. We selected Rfam database to annotate the small RNA sequences obtained by sequencing. rRNA, snoRNA, snRNA, tRNA and other non-mirNA sequences were found and removed as far as possible. identification of miRNAs by compare the precursors to the genome; differential expression analysis of miRNAs; target prediction of miRNAs.
The degradome main steps are below: a) mRNA 3' and 5' adaptor were captured by magnetic beads; b) Mixed reverse transcription of Biotinylated random primers and mRNA; c) PCR amplification. Completed degradome library was sequenced with Illumina Hiseq2000/2500.
Independently developed program ACGT101-DEG was used for degradome sequencing analysis and target genes prediction analysis was performed with CleaveLand program.
Supplementary_files_format_and_content: xls include all miRNA expressed for each Sample;xls include the degradome Identified target genes
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| Submission date |
Feb 15, 2022 |
| Last update date |
Sep 08, 2022 |
| Contact name |
yanyong cao |
| E-mail(s) |
zhangxingrui126@126.com
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| Organization name |
Henan Academy of Agricultural Sciences
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| Street address |
No. 116, Huayuan Road
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| City |
Zhengzhou |
| State/province |
henan |
| ZIP/Postal code |
450000 |
| Country |
China |
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| Platform ID |
GPL17628 |
| Series (1) |
| GSE196738 |
Identification of miRNAs and their target genes associated with improved corn seed vigor induced by gibberellin (GA3) through small RNAs and degradome sequencing |
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| Relations |
| BioSample |
SAMN25963252 |
| SRA |
SRX14186287 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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