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| Status |
Public on Nov 14, 2018 |
| Title |
GA treatment rep2 |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Zea mays |
| Characteristics |
treatment time: 48 h
treatment: gibberellin acid
tissue: embryo
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| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol reagent (Invitrogen) was used to isolate total RNA, and then small RNAs were enriched using polyethylene glycol (PEG8000). For small RNA library construction, enriched small RNAs were ligated with 3’ RNA adapter, and fractionated through 15% denaturing polyacrylamide gel electrophoresis (PAGE). Products with a length of 36 to 44 nucleotides (nt) were ligated with 5’ RNA adapter, and used to perform RT-PCR amplification.
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 |
Cutadapt (version 1.2.1) was used to filter out low-quality sequences, and to find and remove 5’- and 3’-adapter sequences from the raw tags
Tags with the size range of 18-28 nt were retained for subsequent analysis
The clean sequencing tags in fastq format were firstly transformed into fasta format and collapsed to make each sequence entry unique using fastq2fastq and collapse_reads_md scripts in mirdeep2 package, respectively
collapsed tags in fasta format were aligned to the maize B73 reference (v2)using Bowtie (version 0.12.8)
Only tags that matched perfectly to less than 20 genomic regions with 0 mismatch in the Z. mays genome were used for MIRNA annotation
Genome_build: maize B73 reference (v2)
Supplementary_files_format_and_content: tab-delimited text files include count values for each mature miRNA and its precusor
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| Submission date |
Nov 13, 2018 |
| Last update date |
Nov 14, 2018 |
| Contact name |
Shuxin Zhang |
| E-mail(s) |
maizeemsdb@163.com
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| Organization name |
Shandong Agricultural University
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| Street address |
DaiZong Street NO.61
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| City |
Tai'an |
| ZIP/Postal code |
271018 |
| Country |
China |
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| Platform ID |
GPL17628 |
| Series (1) |
| GSE122477 |
Genome-Wide Identification and Characterization of microRNAs responding to ABA and GA in maize embryos during seed germination |
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| Relations |
| BioSample |
SAMN10415311 |
| SRA |
SRX5002123 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3467065_G2-1_mirid.gff_tabled.txt.gz |
194.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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