Dajiao samples at 10 °C for 3 h - SRA

SRX707446: Dajiao samples at 10 °C for 3 h
1 ILLUMINA (Illumina HiSeq 2000) run: 17.1M spots, 1.7G bases, 1.2Gb downloads

Design: Total RNA was extracted from Cavendish and Dajiao leaves (Four biological replicates of Cavendish and Dajiao seedlings at 10 °C for 0, 3 and 6 h) using plant total RNA isolation kit (Tiandz Inc; Beijing, China). RNA degradation and contamination was monitored on 1% agarose gels; RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. All 24 samples had RIN values above 8.0. Sequencing libraries were generated using Illumina TruSeq™ RNA Sample Preparation Kit (Illumia, San Diego, USA) following manufacturer’s recommendations and four index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and enzymes were removed. After adenylation of 3’ ends of DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 200 bp in length the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 10 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2000 platform and 50 bp fragment reads were generated.

Submitted by: INSTITUTE OF FRUIT TREE RESEARCH, GUANGDONG ACADEMY OF AGRICULTURAL SCIENCES (INSTITUTE OF FRUIT TREE RESEARCH, GUANGDONG ACADEM)

Study: 1) Cold-sensitive Cavendish Banana; 2) Cold-tolerant Dajiao Plantain Transcriptome or Gene expression

PRJNA261638 • SRP047347 • All experiments • All runs

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In this study, Dajiao (Musa spp. Dajiao; ABB Group) collected from subtropical region of China with high cold-tolerance was used to investigate responses to cold stress at transcriptional level. A cold-sensitive Cavendish (Musa spp. Cavendish; AAA Group) was also examined as a control. A well-established whole genome transcriptome analysis method, based on RNA-Seq was utilized to reveal the different cold tolerance between Cavendish and Dajiao. Our study provides a broad picture of the Cavendish and Dajiao cold-responsive transcriptomes, and cold-tolerance molecular mechanisms of Dajiao under cold stress.

Sample: Four biological replicates of Dajiao samples at 10 Â¡Ã£C for 3 h

SAMN03074952 • SRS706643 • All experiments • All runs

Organism: Musa acuminata

Library:

Name: Dajiao-Cold-3h

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Spot descriptor:

1 forward

Runs: 1 run, 17.1M spots, 1.7G bases, 1.2Gb

Run	# of Spots	# of Bases	Size	Published
SRR1582388	17,138,985	1.7G	1.2Gb	2015-06-30

ID:: 996479

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