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| Status |
Public on Oct 01, 2015 |
| Title |
Z2-3 |
| Sample type |
SRA |
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| Source name |
Rice leaf
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| Organism |
Oryza sativa |
| Characteristics |
season: dry
field: irrigated
replicate: 2
genotype: Azucena
time point: 3
sampling date: 2013-01-29
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| 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.
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| 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
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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 |
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
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| Submission date |
Sep 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Hafemeister |
| Organization name |
New York Genome Center
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| Lab |
Satija Lab
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| Street address |
101 Avenue of the Americas
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10013 |
| Country |
USA |
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| Platform ID |
GPL13160 |
| Series (1) |
| GSE73609 |
Rice gene expression in irrigated and rainfed fields during two seasons |
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| Relations |
| BioSample |
SAMN04123647 |
| SRA |
SRX1297221 |
| 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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