RNAseq of Apple: Honeycrisp softscald development - SRA

SRX2012894: RNAseq of Apple: Honeycrisp softscald development
1 ILLUMINA (Illumina HiSeq 2500) run: 3.2M spots, 165.7M bases, 136.2Mb downloads

SRX2020807

Design: Strand specific RNAseq library construction - Transcriptomic profiling was performed on 3 composite (3 fruit each) biological replications for each orchard/time point combination using the protocol described by Gapper et al [14]. Briefly, total RNA was extracted using a chloroform phase extraction and purified using a RNAeasy column (Qiagen),.RNA-seq libraries were created using total RNA according to Zhong et al [94]. mRNA was isolated from total RNA, fragmented and used as a template for cDNA synthesis via reverse transcription (Superscript III, Invitrogen). After the first strand of cDNA synthesis, the second strand was synthesized via a dNTP mix utilizing dUTP instead of dTTP. Ends of the double-stranded cDNAs were then repaired (Enzymatics), dA tailed by the Klenow enzyme (Enzymatics), and universal TruSeq adapters (Illumina) were ligated. After ligation, the second strand was digested by uracil DNA glycosylase (UDG) to produce strand-specific enrichment of the library. The UDG-digested cDNA was then used as a template to enrich the libraries by polymerase chain reaction (PCR) using primers containing the TruSeq barcodes, and the high-fidelity enzyme Phusion (NEB) with the conditions described in Gapper et al [14]. 20 ng of the libraries were pooled for sequencing; 48 were multiplexed per sequencing reaction using an Illumina HiSeq 2000/2500 next-generation sequencer at the Weill Medicine School Sequencing Facility (Cornell University, New York City, NY, USA).

Submitted by: Boyce Thompson Institute

Study: Malus domestica cultivar:Honeycrisp Transcriptome or Gene expression

PRJNA338483 • SRP081273 • All experiments • All runs

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'Honeycrisp' is a profitable apple cultivar, which can develop soft scald, a non-pathogenic chilling related necrotic disorder of the peel, reducing storage life. Improved understanding of metabolism associated with the disorder would further basic knowledge of this and other apple fruit chilling injuries and enable better risk management decisions for apple storage. This project involved the profiling of the transcriptome during the etiology of this disorder under cold storage.

Sample:

SAMN05559630 • SRS1610035 • All experiments • All runs

Organism: Malus domestica

Library:

Name: M_2_R1

Instrument: Illumina HiSeq 2500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: other

Layout: SINGLE

Runs: 1 run, 3.2M spots, 165.7M bases, 136.2Mb

Run	# of Spots	# of Bases	Size	Published
SRR4019365	3,249,673	165.7M	136.2Mb	2016-08-24

ID:: 2909411

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