|
| Status |
Public on Mar 23, 2021 |
| Title |
DNA from seed produced at 27°C_Mature stage, T28_M1 |
| Sample type |
SRA |
| |
|
| Source name |
DNA from seed produced at 27°C_Mature stage
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col0
developmental stage: seed Mature stage
treatment: growing severe heat stress conditions 27°C
tissue: entire seed
|
| 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)
|
| 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.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA were extracted from the frozen grinded tissues lots using the Macherey-Nagel NucleoSpin® DNA Food kit following manufacturer’s instructions
DNA samples were sent to to the BGI and library construction, bisulfite treatment using a ZYMO EZ DNA Methylation-Gold kit and paired-end sequencing using an Illumina Hiseq 2500 (PE100 20M)
Library Construction (MGIEasy Whole Genome Bisulfite Sequencing Library Prep Kit) details: Fragment genome DNA to 100-300 bp by Sonication DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adaptors. 1) Bisulfite treatment by ZYMO EZ DNA Methylation-Gold kit. (Unmethylated Lambda DNA, Promega as control) 2) PCR amplification and purification 3) Denaturation 4) ssDNA circularization 5) Enzymatic Digestion and purification 6) Qualified library for sequencing.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
fastQC was used to perform fastq (short reads) quality check
Methypy software (Schultz et al. 2015) was used to mapped reads againt the Arabidopsis genome (TAIR 10) using the paired-end-pipeline (chloroplastic genome was used as negative control then remove duplicated reads, and finally call methylation state for all cytosine (allc files). Bigwig files were generated using Methylpy
Genome_build: TAIR 10
Supplementary_files_format_and_content: bw
|
| |
|
| Submission date |
Feb 22, 2021 |
| Last update date |
Mar 24, 2021 |
| Contact name |
Jerome Verdier |
| E-mail(s) |
[email protected]
|
| Organization name |
INRAE / IRHS
|
| Lab |
SEED
|
| Street address |
Rue Georges Morel
|
| City |
Angers |
| ZIP/Postal code |
49000 |
| Country |
France |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE167243 |
Bisulfite sequencing (WGBS) of Arabidopsis seed developmental stages at different degrees of heat stress |
| GSE167245 |
Regulation of DNA (de)methylation positively impacts seed germination during seed development under heat stress |
|
| Relations |
| BioSample |
SAMN18027697 |
| SRA |
SRX10150975 |
