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| Status |
Public on Aug 18, 2020 |
| Title |
mRNA_Blade_S3_rep1 |
| Sample type |
SRA |
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| Source name |
blade
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| Organism |
Oryza sativa |
| Characteristics |
tissue: blade
developmental stage: S3
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| Growth protocol |
The seeds were soaked in distilled water at room temperature for 1 day and imbibed for 2 days in water at 37°C in a constant temperature incubator (referred to as the first and second day after germination, respectively). The water was changed twice daily. The germinated seeds were transferred to 96-well plates with cut bottoms and grown in water under a 16 h (light, 28°C)/8 h (dark, 25°C) cycle.
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| Extracted molecule |
total RNA |
| Extraction protocol |
LJ and blade tissue form the first complete leaves of seedlings were separately cut and collected on the 4th, 5th, 6th, 7th, and 9th day after germination, the length of LJ were less than 1 mm, and the length of blade was less than 10 mm. The collected tissues were immediately frozen in liquid nitrogen and subjected to total RNA extraction with TRIzol (Invitrogen). The NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used with 3 ug of total RNA per sample to constructed RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Basecalls performed using CASAVA version 1.8
After removing low-quality reads, the clean reads were trimmed with Trimmomatic-0.36 and then mapped to the rice reference genome rice IRGSP-1.0 with TopHat v2.1.1(defaut parameters)
The uniquely mapped reads were used to calculate FPKM (fragments per kilobase of transcript per million reads) values for the genes with Cufflinks v2.2.1 (Trapnell et al., 2012) to estimate their expression levels in different samples.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample of RNA-seq
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| Submission date |
Aug 09, 2020 |
| Last update date |
Aug 19, 2020 |
| Contact name |
Chang Liu |
| E-mail(s) |
cliu2020@126.com
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| Organization name |
Huazhong Agricultural University
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| Street address |
Shizishan Street
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| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL23013 |
| Series (2) |
| GSE155930 |
Spatiotemporal resolved leaf angle establishment improves rice grain yield via controlling population density [mRNA] |
| GSE155932 |
Spatiotemporal resolved leaf angle establishment improves rice grain yield via controlling population density |
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| Relations |
| BioSample |
SAMN15769286 |
| SRA |
SRX8912723 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4716039_B3_rep1.txt.gz |
352.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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