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Sample GSM1091765

Query DataSets for GSM1091765

Status

Public on Mar 02, 2013

Title

Sample type

SRA

Source name

in-vitro germinated pollens

Organism

Zea mays

Characteristics

inbred line: B73
tissue: in-vitro germinated pollens

Extracted molecule

total RNA

Extraction protocol

Mature pollens (MP) were collected by shaking tassels at 9:00-10:00 a.m. To ensure the viability of collected pollens, we tested the percentage of in vitro germination. Only pollen grains with germination percentage greater than 90% were used. Germinated pollens (GP) were obtained after culturing 30 min in liquid media, with a germinated percentage greater than 90%. Silks with approximately 5 cm out of the bracts were harvested as mature silks (MS). To obtain pollinated silks (PS), mature silks were pollinated by an overdose of active pollens. Thirty min later, most pollen grains germinated and their tubes penetrated into silk tissues. Then, the pollinated silks were harvested after shaking off un-adhered pollen grains.
Briefly, total RNA was isolated using Trizol reagent. Small RNAs ranging from 18-30 nt were gel-purified and ligated to proprietary adapters at the 5' and 3' termini. RT-PCR was performed with 18 cycles, and the products were purified and used for Solexa sequencing.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina Genome Analyzer IIx

Data processing

Illumina Casava1.7 software used for basecalling.
Unique reads were mapped onto the genome using the program SOAP3
The perfectly matched reads were searched against the Metazoa mature micorRNA of Sanger miRBase4 (Release 18) using the software Patscan12.
The inverted repeats (step loops or hairpin structure) were found using software Einverted of Emboss9, with the parameters threshold = 30, match score = 3, mismatch score = 3, gap penalty = 6, and maximum repeat length = 240
Secondary structure of the inverted repeat was predicted by RNAfold
Inverted repeats of secondary structure were evaluated by MirCheck10 using modified parameter
Genome_build: Sanger miRBase 18.0
Supplementary_files_format_and_content: excel file includes miRNA name, length, reads number, TPM(RPKM), significance analysis and target genes prediction for each sample.

Submission date

Mar 01, 2013

Last update date

May 15, 2019

Contact name

Xiaoming Li

E-mail(s)

lxmlmh@163.com

Organization name

Shandong Agriculutural University

Street address

61st ,Daizong Street