GSM3486956: NM3; Triticum aestivum; RNA-Seq - SRA

SRX5057643: GSM3486956: NM3; Triticum aestivum; RNA-Seq
1 ILLUMINA (Illumina Genome Analyzer) run: 21.7M spots, 6.5G bases, 2.6Gb downloads

Submitted by: NCBI (GEO)

Study: Molecular signal communication in soil during arbuscular mycorrhizal formation changes the transcriptome profiles in wheat (Triticum aestivum L.) roots

PRJNA506702 • SRP170416 • All experiments • All runs

show Abstracthide Abstract

We aimed to test the hypothesis that the transcriptional profile of wheat roots can be changed by the AM symbiotic signals, even though there is no physical contact with AM fungi. A total of 2,360 differentially expressed genes (DEGs), including 1,888 up-regulated DEGs and 472 down-regulated DEGs were found. Among them, 59 were highly induced DEGs (gene expression fold changed > 500), and 121 genes only expressed in the NM treatment. The DGEs covered all the 21 chromosomes of wheat genome, and were dominantly distributed on the 2A, 2B, 2D, 3B, 5B and 5D chromosomes. Most of the DEGs located at membrane, and functioned in catalytic activity, transferase activity and binding. 63 orthologues of the previously reported genes wich play important roles during AM symbiosis in model plants were found. Overall design: 6 samples for the two treatments, and three biological replicates for each treatment

Sample: GEO accession GSM3486956 is currently private and is scheduled to be released on Nov 24, 2018.

SAMN10471542 • SRS4073845 • All experiments • All runs

Organism: Triticum aestivum

Library:

Instrument: Illumina Genome Analyzer

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction protocol: Total RNA was extracted from approximately 100 mg of wheat root of three biological replicates of the two treatments using the RNeasy Plant Mini Kit (Qiagen, USA). according to the manufacturer's instructions.The concentration and quality of the total RNA were estimated using a NanoDrop Spectrometer (Thermo; USA) and verified using agarose gel electrophoresis and an Agilent 2100 bioanalyzer (Agilent, USA). mRNA of each sample was respectively enriched by Oligo(dT) beads, then the enriched mRNA was fragmented into short fragments (~300bp) using fragmentation buffer, followed by reverse transcription into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis. Six independent complementary DNA (cDNA) libraries corresponding to the three biological replicates for each treatment were constructed. cDNA library quality and fragment length were verified using an Agilent 2100 bioanalyzer and real-time PCR. Fragment length distributions were within the expected ranges according to the CLC Sequence Viewer software, and the average read length was 150 bp.

Experiment attributes:

GEO Accession: GSM3486956

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 21.7M spots, 6.5G bases, 2.6Gb

Run	# of Spots	# of Bases	Size	Published
SRR8239379	21,691,685	6.5G	2.6Gb	2018-11-26

ID:: 6813243

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