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Sample GSM3061086 Query DataSets for GSM3061086
Status Public on Mar 22, 2019
Title la_p_cluster_1
Sample type SRA
 
Source name la_p_cluster_1
Organism Lupinus albus
Characteristics group: Root Clusters of P Deprived Roots
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from three biological replicates of 12 root samples apices for control plants and apices and cluster root for Pi and Fe deficient plants using the Spectrum™ Plant Total RNA Kit (Sigma Aldrich ).
cDNA library preparation and sequencing reactions were performed by IGA Technology Services s.r.l. (Udine, Italy). An amount of 2 μg of total RNA was used for library preparation following the Illumina protocol TrueSeq 2.0. Briefly, RNA was fragmented into fragment with an average of 500 bp. Then, mRNA was purified using poly-T beads. The first- and second-strand cDNAs were synthesized and end repaired. Adaptors were ligated after adenylation at the 3’ ends and cDNA templates were enriched by PCR. The 50 bp single end reads were obtained using an Illumina Hiseq2000 platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Adapter Removal, Cutadapt v.1.11, Default parameters
Trimming, ERNE-filter v.1.4.6, default parameters
Alignment to Transcriptome Reference, TopHat V.2.0.5, default parameters
Transcript Quantification, Cufflinks V2.0.2, default parameters
Differential Expression analysis, Cuffdiff V2.0.2, default parameters
Genome_build: Transcriptome Build LAGI02, available as supplementary data at https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-230
Supplementary_files_format_and_content: We provide as processed data file the cuffdiff output of differential expression analysis
 
Submission date Mar 22, 2018
Last update date Mar 22, 2019
Contact name Fabio Marroni
Organization name Università di Udine
Department DI4A
Street address Via delle Scienze 208
City Udine
ZIP/Postal code 33100
Country Italy
 
Platform ID GPL23437
Series (1)
GSE112220 Physiological and transcriptomic characterization of white lupin response to Fe deficiency
Relations
BioSample SAMN08773666
SRA SRX3832728

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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