RNA-seq analysis of Phaseolus vulgaris cv. Negro jamapa - SRA

SRX695918: RNA-seq analysis of Phaseolus vulgaris cv. Negro jamapa
1 ILLUMINA (Illumina HiSeq 1000) run: 27.4M spots, 987.2M bases, 548.3Mb downloads

Design: Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools.

Submitted by: USDA-ARS, UNIVERSITY OF MINNESOTA

Study: RNA-seq analysis of Phaseolus vulgaris cv. Negro jamapa

PRJNA210619 • SRP046307 • All experiments • All runs

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We present the Phaseolus vulgaris cv. Negro jamapa expression profiles for all predicted genes in the P. vulgaris reference genome (G 19833) for 24 unique samples from seven distinct tissues; roots, nodules, stems, flowers, leaves, pods, and seeds throughout development. We identified genes differentially expressed between distinct tissues and between samples from the same tissue collected at different time points. We have also identified sequences uniquely expressed in each sample and in each tissue. Genes with stable expression patterns, to be used as housekeeping sequences in future experiments, were also identified. We utilized the expression profiles of all predicted genes in Phaseolus vulgaris to examine the biological processes related to seed and pod development, nodulation and symbiosis, and changes in gene expression due to nitrogen availability.

Sample: Generic sample from Phaseolus vulgaris

SAMN02226085 • SRS697027 • All experiments • All runs

Organism: Phaseolus vulgaris

Library:

Name: PvR5

Instrument: Illumina HiSeq 1000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: PolyA

Layout: SINGLE

Spot descriptor:

1 forward

Runs: 1 run, 27.4M spots, 987.2M bases, 548.3Mb

Run	# of Spots	# of Bases	Size	Published
SRR1569476	27,423,246	987.2M	548.3Mb	2015-07-22

ID:: 980347

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