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Sample GSM1202204

Query DataSets for GSM1202204

Status

Public on Jan 01, 2014

Title

mixed tissues for small RNA sequencing

Sample type

SRA

Source name

young leaves, young stems and flower buds

Organism

Prunus persica

Characteristics

cultivar: Lovell
tissue: young leaves, young stems and flower buds

Treatment protocol

None

Growth protocol

Prunus persica cv. Lovell peach trees were grown in the garden of Nanjing Agricultural University, China

Extracted molecule

total RNA

Extraction protocol

A low molecular weight (LMW) RNA was isolated from mixed tissues (peach leaves, young stems and flowers) by using CTAB reagent according to the procedure previously described (Wang X, Xiong A, Yao Q, Zhang Z, Qiao Y (2009) Direct isolation of high-quality low molecular weight RNA of pear peel from the extraction mixture containing nucleic acid. Molecular Biotechnology 44: 61-65). The sample was sequenced by the Beijing Genomics Institute (BGI) (Shenzhen, Guangdong Province, China) using the high-throughput pyrosequencing technology developed by Solexa.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina Genome Analyzer IIx

Data processing

After removing low quality reads and trimming adaptor sequences, the high-quality small RNA reads ranging from 18 to 30 nucleotides were obtained from the sRNA raw data. Small RNA sequences matching non-coding rRNA, tRNA, snRNA and snoRNA in the Rfam 10 (http://www.sanger.ac.uk/resources/databases/rfam.html) and NCBI Genbank databases were removed. The remaining sequences were searched against the miRBase database v18.0 (http://www.mirbase.org, release 18) with up to two mismatches, to identify conserved miRNAs. The sequences that did not map to any miRNAs in miRBase were analysed for predictions to identify novel miRNAs by the program MIREAP (developed by BGI) with default parameters for mapping the peach genome and obtaining all candidate precursors with hairpin-like structures of novel miRNA candidates. Secondary structures of novel miRNAs were also checked using Mfold 3.2.
genome_build: miRBase Release 18
After removing low quality reads and trimming adaptor sequences, the high-quality small RNA reads ranging from 18 to 30 nucleotides were obtained from the sRNA raw data.
Small RNA sequences matching non-coding rRNA, tRNA, snRNA and snoRNA in the Rfam 10 (http://www.sanger.ac.uk/resources/databases/rfam.html) and NCBI Genbank databases were removed.
The remaining sequences were searched against the miRBase database v18.0 (http://www.mirbase.org, release 18) with up to two mismatches, to identify conserved miRNAs.
The sequences that did not map to any miRNAs in miRBase were analysed for predictions to identify novel miRNAs by the program MIREAP (developed by BGI) with default parameters for mapping the peach genome and obtaining all candidate precursors with hairpin-like structures of novel miRNA candidates
Secondary structures of novel miRNAs were also checked using Mfold 3.2
Genome_build: miRBase Release 18
Supplementary_files_format_and_content: all of processed data files format are fasta and content is: one small RNA library and three degradome libraries

Submission date

Aug 06, 2013

Last update date

May 15, 2019

Contact name

Zhihong Gao

E-mail(s)

[email protected]

Phone

0086-25-84395724

Organization name

Nanjing Agricultural University