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Sample GSM2065727

Query DataSets for GSM2065727

Status

Public on Jul 22, 2016

Title

Rep_1 9 DL

Sample type

SRA

Source name

drought_lower_9 days

Organism

Setaria viridis

Characteristics

plant condition: drought (D) treated
tissue: Lower region (crown)
harvest time point: 9 days after sowing
biological replicate: Rep_1

Growth protocol

Seeds were grown in 25% sand, 75% peat in Deepots; 20 plants per sample were harvested.

Extracted molecule

total RNA

Extraction protocol

Total RNA was purified by Zymo Plant RNA kit
Ribosomal RNA was depleted by Ribozero Plant Root/Seed kit, strand-specific libraries were made using NEBNext Ultra Directional kit for Illumina; libraries were amplified with 6 bp barcoded pcr primers
12 libraries were pooled per lane; aimed for 10 million reads per library.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

All RNA-Seq data was quality controlled via fastqc, adapters were filtered using cutadapt, low-quality 3’ sequences were filtered utilizing the fastx toolkit (discarding nucleotides < Q35, reads shorter than 50nt), and read singletons were discarded.
Read pairs which survived the above process were aligned against the Setaria viridis v1.1 genome
Alignments of RNA-Seq data were grouped by tissue/treatment/duration combinations (e.g. the three biological replicates derived from well-watered upper roots samples 6DAS were treated as a group).
Replicate groups were compared utilizing the cuffdiff algorithm
Differentially expressed genes were grouped by their directionality of differential expression, and analyzed for overrepresentation of Gene Ontology terms (GO terms) (Ashburner et al., 2000) utilizing the ‘topGO’ R package (Alexa, Rahnenführer, & Lengauer, 2006) from Bioconductor (Gentleman et al., 2004). GO-terms with a false-discovery corrected p-value <0.05 were deemed to be over-represented.
Genome_build: Setaria viridis v1.1 genome (http://phytozome.jgi.doe.gov/)
Supplementary_files_format_and_content: tab-delimited text files include log2 fold change values for each Sample
Supplementary_files_format_and_content: GO enrichment csv files include GO term, p-value and false discovery rate for each Sample (GO.tar.gz)

Submission date

Feb 18, 2016

Last update date

May 15, 2019

Contact name

Jose Ramon Dinneny

E-mail(s)

jdinneny@carnegiescience.edu

Organization name

Carnegie Institution for Science, Department of Plant Biology

Department

Plant Biology