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| Status |
Public on Jun 24, 2021 |
| Title |
MC1_transcriptome |
| Sample type |
SRA |
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| Source name |
0 μΜ cadmium_shoot
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| Organism |
Oryza sativa |
| Characteristics |
cultivar: Zhong Jiazao-17
tissue: Shoot
cadmium treatment: 0 μΜ cadmium treatment for 12 days
development stage: rice at one leaf stage
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| Treatment protocol |
Once the first leaf was fully expanded, seedlings were subjected to CdCl2•2.5H2O in different concentrations, including 0 µM (the control, MC) and 100 µM (MS) for 12 days, in triplicate.
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| Growth protocol |
Germinating seedlings were removed to a hydroponics solution consisting of Hoagland’s solution (pH 5.5) in a climate chamber (relative humidity 80%, 30/28℃ day/night temperature)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
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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| Description |
MC1_MC_FPKM
MC1_Clean_Data1
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Jun 25, 2018 |
| Last update date |
Jun 24, 2021 |
| Contact name |
Min Zhong |
| E-mail(s) |
zhongmin2007@163.com
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| Organization name |
China National Rice Research Institute
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| Street address |
Rice research road NO.28
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| City |
Fu Yang |
| State/province |
Hang Zhou |
| ZIP/Postal code |
311400 |
| Country |
China |
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| Platform ID |
GPL23013 |
| Series (2) |
| GSE116214 |
An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [transcriptome] |
| GSE116275 |
An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress |
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| Relations |
| BioSample |
SAMN09479328 |
| SRA |
SRX4290730 |
| 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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