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Sample GSM1899189 Query DataSets for GSM1899189
Status Public on Oct 01, 2015
Title X2-9
Sample type SRA
 
Source name Rice leaf
Organism Oryza sativa
Characteristics season: dry
field: irrigated
replicate: 1
genotype: Azucena
time point: 9
sampling date: 2013-02-10
Growth protocol The rice plants were grown at IRRI in a 25 x 90 m field divided into equal size rainfed and irrigated sub-fields. The dry season and wet season experiments took place during the months of January-February 2013 and July-August 2013, respectively.
Extracted molecule total RNA
Extraction protocol Frozen leaf tissue was ground manually with a mortar and pestle cooled in liquid nitrogen. Total RNA was extracted from about 200 to 400 µL of ground tissue using the RNeasy® Plant Mini Kit following manufacturer's instructions.
RNA treated with Baseline-ZERO Dnase, depleted of ribosomal RNA using Epicentre® Ribo-Zero Magnetic Kit for plant leaf tissue. Libraries constructed RNA libraries using the Epicentre® ScriptSeqTM v2 RNA-Seq Library Preparation Kit.
RNA-Seq, using HiSeq® 2000, 51 bp paired-end sequencing, with either 6 or 8 libraries per lane
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Reads aligned to the O. sativa Nipponbare - release 7 of the MSU Rice Genome Annotation Project reference genome - including 12 rice chromosomes, chloroplast, mitochondrion, Syngenta pseudomolecule, and the unanchored BAC pseudomolecule using Tophat version 2.0.6, discarding low-quality alignments (quality score below 1)
Counting number of reads that uniquely mapped to genes using HTSeq version 0.6.1
Normalization: compensation for variable sequencing depth between samples using the median-of-ratios method of DESeq2 version 1.6.3 and variance stabilizing transformation provided by the same package. The minimum expression value was subtracted so that zero read counts had an expression value of zero.
Genome_build: Release 7 of the MSU Rice Genome Annotation Project reference genome
Supplementary_files_format_and_content: tab-delimited text files with normalized read counts for each sample
 
Submission date Sep 30, 2015
Last update date May 15, 2019
Contact name Christoph Hafemeister
Organization name New York Genome Center
Lab Satija Lab
Street address 101 Avenue of the Americas
City New York
State/province NY
ZIP/Postal code 10013
Country USA
 
Platform ID GPL13160
Series (1)
GSE73609 Rice gene expression in irrigated and rainfed fields during two seasons
Relations
BioSample SAMN04123624
SRA SRX1297108

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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