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Status |
Public on Mar 22, 2019 |
Title |
la_p_cluster_1 |
Sample type |
SRA |
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Source name |
la_p_cluster_1
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Organism |
Lupinus albus |
Characteristics |
group: Root Clusters of P Deprived Roots
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
Mar 22, 2018 |
Last update date |
Mar 22, 2019 |
Contact name |
Fabio Marroni |
Organization name |
Università di Udine
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Department |
DI4A
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Street address |
Via delle Scienze 208
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City |
Udine |
ZIP/Postal code |
33100 |
Country |
Italy |
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Platform ID |
GPL23437 |
Series (1) |
GSE112220 |
Physiological and transcriptomic characterization of white lupin response to Fe deficiency |
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Relations |
BioSample |
SAMN08773666 |
SRA |
SRX3832728 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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