RNA-seq of Hordeum vulgare inoculated with Cochliobolus sativus: Samp... - SRA

SRX1660120: RNA-seq of Hordeum vulgare inoculated with Cochliobolus sativus: Sample INOC_MUT_12
1 ILLUMINA (Illumina HiSeq 2000) run: 18.9M spots, 3.8G bases, 2.4Gb downloads

Design: "Barley (Hordeum vulgare) seedlings were grown for 14 days until the second leaf was fully expanded. The two genotypes were the cultivar Morex (resistant, WT) and a gamma radiation-induced Morex mutant (susceptible, MUT) that had been selfed 4 times from the time of mutagenesis. Each genotype was treated with (INOC) and without (MOCK/water) the pathogen Cochliobolus sativus isolate ND85F. Tissue was harvested from the second leaves of 5 seedlings at 12, 24, and 36 hours after inoculation for each genotype and treatment and immediately frozen in liquid nitrogen. There were 3 biological replicates for a total of 36 samples. For RNA extraction, 1g of plant tissue was ground to a fine powder under liquid nitrogen. RNA was extracted by the Trizol method. RNA samples were purified with RNeasy purification columns from Qiagen. Samples were checked for quality and integrity with the Agilent Bioanalyzer 2100 prior to sequencing. The project was sequenced on a HiSeq 2000 machine (100 PE) except for sample R3_INOC_MUT_24 which was re-sequenced on a HiSeq 2500 machine due to an error by the Genomics Center that lead to the initial R3_INOC_MUT_24 sample being sequenced incorrectly. Libraries were created using the TruSeq RNA v 2 library kits and multiplexed into 3 pools. Pools 1 and 2 had 10 samples each and pool 3 has 16 samples. Pools 1 and 2 were loaded across 2 lanes of the flow cell while pool 3 was loaded across 3 lanes. This is why there are multiple forward and reverse reads for each sample, which must be concatenated prior to further processing. (These are raw .fastq reads.) R3_INOC_MUT_24 has just one forward and one reverse read since it was sequenced separately. It is also at a greater depth. Average quality scores are above Q30. Libraries were gel size selected to have inserts of ~200 bp."

Submitted by: University of Minnesota

Study: Hordeum vulgare subsp. vulgare cultivar:Morex Transcriptome or Gene expression

PRJNA315041 • SRP071745 • All experiments • All runs

show Abstracthide Abstract

The purpose of this study was to characterize the transcriptomic response of Morex (which carries durable resistance to Cochliobolus sativus Isolate ND85F) to a susceptible Morex mutant.

Sample: Sample 4

SAMN04549450 • SRS1338312 • All experiments • All runs

Organism: Hordeum vulgare subsp. vulgare

Library:

Name: R2_INOC_MUT_12.2

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: RANDOM

Layout: PAIRED

Spot descriptor:

1 forward101 reverse

Runs: 1 run, 18.9M spots, 3.8G bases, 2.4Gb

Run	# of Spots	# of Bases	Size	Published
SRR3290277	18,914,936	3.8G	2.4Gb	2017-01-01

ID:: 2378819

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Search details

Recent activity