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| Status |
Public on Mar 23, 2021 |
| Title |
RNAs from seed produced at 23°C_germination IV stage, ros_1 |
| Sample type |
SRA |
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| Source name |
RNAs from seed produced at 23°C_germination IV stage
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: ros1-4
developmental stage: seed germination IV stage
treatment: growing control conditions 23°C
tissue: entire seed
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| Treatment protocol |
After bolting and first flowers, control plants were grown at the same temperature condition 24°C/22°C (23°C) but stressed plants were transferred to another culture room with mild stress conditions 26°C/24°C (25°C) and severe stress conditions 28°C/26°C (27°C)
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| Growth protocol |
Plants were grown in a culture room in trays containing a sterile soil at 20°C/18°C, with a 16 h light photoperiod at 200 μmol photons m -²s-².
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from the frozen grinded tissues lots using the Macherey-Nagel NucleoSpin RNA Plus kit (Macherey-Nagel, GmbH & Co. KG, Germany) following manufacturer’s instructions
Samples were sent to BGI, Hong Kong, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 24M reads of 50bp per sample
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Genome mapping against Arabidopsis reference transcriptome Araport v11 using Salmon algorithm
Clean reads were mapped to the reference transcriptome araport v11 and quantified using Salmon algorithm to calculate gene expression level in counts
Genome_build: Araport11_genes.201606.cdna.fasta downlaoded from arabidopsis.org
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample
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| Submission date |
Feb 22, 2021 |
| Last update date |
Mar 23, 2021 |
| Contact name |
Jerome Verdier |
| E-mail(s) |
[email protected]
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| Organization name |
INRAE / IRHS
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| Lab |
SEED
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| Street address |
Rue Georges Morel
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| City |
Angers |
| ZIP/Postal code |
49000 |
| Country |
France |
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| Platform ID |
GPL24025 |
| Series (2) |
| GSE167244 |
RNA sequencing of Arabidopsis mature seed and germination stages |
| GSE167245 |
Regulation of DNA (de)methylation positively impacts seed germination during seed development under heat stress |
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| Relations |
| BioSample |
SAMN18027722 |
| SRA |
SRX10151007 |
| 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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