GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM1398436

Query DataSets for GSM1398436

Status

Public on Dec 30, 2014

Title

HHZ_1d-2

Sample type

SRA

Source name

HHZ_1d-2_leaves

Organism

Oryza sativa

Characteristics

genotype: recurrent parent
Stage: tillering phase
treatment: drought treatment for 1 day
tissue: leaf

Treatment protocol

The drought stress treatment was started by withholding water at the tillering stage.The days were counted after the AWC in the soil reached 20% to allow drought measurements at precisely determined intervals, and the soil water content reached 15%, 10% and 7.5% after 1d, 3d and 4d drought treatment, respectively.

Growth protocol

A pot experiment was arranged in a randomized complete block design with three treatments (well-watered, 1d drought stressed, and 3d drought stressed) and two replications (3 pots/replication) in a greenhouse at the Institute of Crop Sciences of Chinese Academy of Agricultural Sciences (CAAS) (Beijing, China). Three strong seedlings of the three genotypes were equidistantly transplanted into a strip pot (15 cm in height and 50 cm in diameter) ﬁlled with 2 kg of sterilized ﬁeld soil, which contained about 50% available water content (AWC) of the soil measured by soil moisture meters (TZS-W). Seedling of each genotype were planted in 6 pots giving a total of 6 plants; all plants were grown with 14 h daylight at 28 °C and an 10 h dark period at 25 °C under controlled conditions.

Extracted molecule

total RNA

Extraction protocol

For all RNA-seq samples, total RNA was extracted with TRIzol Reagent (Invitrogen, Carlsbad, California, USA), and quantified using a Qubit RNA assay kit (Applied Biosystems, Foster City, California, USA). RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA). RNA samples from three independent replicates for each treatment were pooled.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

CP1D1

Data processing

Primary data analysis and base calling was performed by the Illumina instrument software.
Low quality nucleotides (< Q20) were trimmed from raw sequences for each sample, and then pair-end reads with either of both with length less than 30 bp were removed using an in-house Perl script.
The raw reads were first filtered by removing adaptor sequences and low-quality sequences by using in-house perl script. The retained high quality pair-end reads of rice for each sample were mapped to the rice genome of RGAP at MSU (Kawahara et al., 2013) by tophat (Trapnell et al., 2009) and then assembled with Cufflinks (Trapnellet al., 2010) to construct unique transcipts sequences, using the parameter:-g -b -u -o.
Cuffcompare (Trapnell et al., 2009) was used to compare the assembled transfrags of each sample to the reference annotation, and build up a non-redundant transcripts data set among the samples. The number of mapped clean reads for each gene was counted and normalized into RPKM value (Mortazavi et al., 2008)
Genome_build: Nipponbare
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample with replicates merged.

Submission date

May 23, 2014

Last update date

May 15, 2019

Contact name

Fan Zhang

Organization name

CAAS

Street address

12 South Zhong-Guan-Cun St.

City

Beijing