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Status |
Public on Jun 01, 2017 |
Title |
JS_RNA-seq |
Sample type |
SRA |
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Source name |
Callus
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Organism |
Oryza sativa Japonica Group |
Characteristics |
rice cultivar: Tainung 67 tissue culture stage: Successful Regeneration time point: TS
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Treatment protocol |
The callus samples were collected at different time points of culture starting with embryonic stage (T0). N6D medium was used for callus induction of both cultivars; induced calli were transferred to fresh N6D medium for subsequent callus growth. Finally calli were transferred to REIII M2 medium (MS salt with vitamin, 1g/L casein hydrolysate, 3% sucrose, 3% sorbitol, 0.02 mg/L NAA, 2mg/L BAP, pH5.8 0.4% gelrite) for regeneration.
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Growth protocol |
Seeds of TNG67 and IR64 were surface-sterilized in 70% ethanol for 1 min and rinsed with distilled water. The sterilized seeds were soaked in 2.5% sodium hypochlorite (NaClO; The Clorox Co., Oakland, CA, USA) containing 0.2% Tween 20 (Sigma-Aldrich, St. Louis, MO, USA) for 15 min in a rotator followed by washing with sterile ddH2O. After surface sterilization, seeds were sown on N6D media (N6 salt, Vitamin B5, 3% sucrose, 2.5 mg/L 2,4-D pH 5.8 0.4% gelsite) for callus induction.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted & quantified using Qubit RNA assay 100 ng RNA was used as starting material for each sample. Total RNA are treated with DNase I (Roche), and cleaned up with phenol-chloroform and precipitated with ethanol. RNA–Seq libraries were prepared following standard Illumina protocols. Resulted libraries were then subjected to PCR amplification prior to sequencing on the Illumina HiSeq 2000 sequencers (at National Center for Genome Medicine, Academia Sinica). The quality of reads was checked with FastQC (Andrews, 2010), reads were mapped to Os-Nipponbare-Reference-IRGSP-1.0 using Bowtie (Langmead et al., 2009) allowing two mismatches and only unique alignments were retained. The resulted alignment file was processed and differential expression was calculated using Tophat (Langmead et al., 2009) to generate Fragments Per Kilo Base Per Million mapped reads (FPKM) per gene by applying 4-fold cut-off.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
RNA-Seq
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Data processing |
The quality of reads was checked with FastQC (Andrews, 2010), reads were mapped to Os-Nipponbare-Reference-IRGSP-1.0 using Bowtie (Langmead et al., 2009) allowing up to two mismatches and only unique alignments were retained. The alignment file was processed and differential expression was calculated using Tophat (Langmead et al., 2009) to generate Fragments Per Kilo Base Per Million mapped reads (FPKM) per gene by applying 4-fold cut-off . We identified differentially expressed genes (DEGs) using Tophat to generate Fragments Per Kilo Base Per Million mapped reads (FPKM) per gene. The transcripts showing at least four-fold change with P-value less than 0.05 were identified as DEGs. genome build: MSU7 processed data files format and content: Excel file with FPKM values.
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Submission date |
Jun 01, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Moloya Gohain |
E-mail(s) |
moloyandri@gmail.com
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Organization name |
ACADEMIA SINICA
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Department |
INSTITUTE OF PLANT AND MICROBIAL BIOLOGY
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Lab |
DR. PAO-YANG CHEN LABORATORY
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Street address |
128, SEC.2 ACADEMIA ROAD, NANGANG DISTRICT
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City |
Taipei |
State/province |
Taipei |
ZIP/Postal code |
11529 |
Country |
Taiwan |
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Platform ID |
GPL13834 |
Series (1) |
GSE82138 |
Dynamics of the transcriptome and methylome during the regeneration of rice |
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Relations |
BioSample |
SAMN05195285 |
SRA |
SRX1815132 |
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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