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Sample GSM1202207

Query DataSets for GSM1202207

Status

Public on Jan 01, 2014

Title

ppe degradome flower

Sample type

SRA

Source name

flowers

Organism

Prunus persica

Characteristics

cultivar: Lovell
tissue: flowers

Treatment protocol

None

Growth protocol

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

Extracted molecule

polyA RNA

Extraction protocol

degradome cDNA libraries construction protocol: German MA, Luo S, Schroth G, Meyers BC, Green PJ (2009) Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc 4: 356-362. The construction of degradome libraries differed considerably from past efforts and followed the procedure of as Ma et al. (Ma Z, Coruh C, Axtell MJ (2010) Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell 22: 1090-1103.) with some modifications. (1) Approximately 150 ng of poly (A)+ RNA was used as input RNA and for annealing with biotinylated random primers; (2) Strapavidin capture of RNA fragments was performed via Biotinylated Random Primers; (3) 5´ adaptor ligation was only performed to those RNAs containing 5´-monophosphates; followed by (4) reverse transcription and PCR; (5) libraries were sequenced using the 5´ adapter only, resulting in the sequencing of the first 36 nucleotides of the inserts that represented the 5´ ends of the original RNAs.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina Genome Analyzer IIx

Data processing

Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module. A Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.
genome_build: The peach genome sequences, CDS sequences and gene annotation information were obtained from GDR (www.rosaceae.org).
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