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| Status |
Public on Oct 03, 2017 |
| Title |
G5 progeny, repeated drought stress, 4 week old Col-0, biological rep3 |
| Sample type |
SRA |
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| Source name |
4 week old Col-0
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| Organism |
Arabidopsis thaliana |
| Characteristics |
age: 4 weeks old
tissue: whole rosette
stress: repeated drought stress
ecotype: Col-0
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| Treatment protocol |
For excess-light treatments, exposure to approximately 10X growth irradiance (1000 μ mol photons m-2 s-1) was applied using a mixture of 250W metal halide lamps (Venture Lighting, MH 250W/U) and high pressure sodium lamps (Phillips, SON-T 250W E E40 SL/12) providing a source of ‘warm’ light (similar to sunlight). This was applied for one hour repeated thrice daily at 9:30 am, 1:30pm, and 5:30 pm.
For lineages exposed to drought, stress was applied twice every generation. The first was applied at 2 weeks of age, which involved saturating to field capacity on day 0 and subsequently withholding watered for 2 weeks. Plants were then watered and allowed to recover for 5 days. The drought treatment was repeated following recovery, however, this time for only 12 days to minimise plant death. Plants were then watered until rosette leaf senescence and the appearance of dried, mature siliques for seed harvesting following ABRC guidelines.
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| Growth protocol |
Plants grown on soil, with approximately 3g/L osmocote fertilizer, under a 12-hour photoperiod of 100-150μ mol photons m-2 s -1, 20 (±0.5) °C, and 55 (±5) % RH.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Qiagen DNeasy Plant Mini Kit (Limburg, Netherlands), as per the manufacturer’s instructions. 100-200 ng of fragmented (Covaris) and purified gDNA was bisulfite converted using the Zymo DNA-Gold bisulfite conversion kit (Zymo Research; CA, USA)
Whole genome bisulfite sequencing libraries were constructing using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences; MI, USA) as per the manufacturer’s instructions.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Raw sequencing reads were quality controlled and trimmed using Trim Galore! (v0.3.7), Cutadapt (v1.9), and FastQC (v0.11.2)
Reads were then aligned to TAIR10 using the Bismark aligner (v0.14.5) with the flags --bowtie1 -n 2, -l 20 (bowtie v1.1.2).
Methylated cytosines were extracted, at single cytosine resolution, from aligned reads using the Bismark methylation extractor with default parameters.
The proportion of genome-wide CG, CHG, and CHH methylation was determined as mean methylation across reads at single cytosine resolution (.bed) and across 100 bp windows (.100bp.bed) for genome wide comparisons.
Genome_build: TAIR10
Supplementary_files_format_and_content: 100bp.bed: genome wide mean methylation summarised into 100bp windows. Column headers are as follows: Chromosome, position, length, Proportion methylated C, Number of C's methylated, Number of C's unmethylated, Total C's, Number of C's in region.
Supplementary_files_format_and_content: .bed: mean methylation at single cytosines. Separate files have been produced for each sequence of DNA methylation: CG, CHG, and CHH.
Supplementary_files_format_and_content: .cov: coverage files giving proportion methylation, counts methylated, and counts unmethylated for single cytosines. Separate files have been produced for each sequence of DNA methylation: CG, CHG, and CHH.
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| Submission date |
Jan 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Diep R Ganguly |
| E-mail(s) |
dganguly@sas.upenn.edu
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| Phone |
+1 215-898-0808
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| Organization name |
University of Pennsylvania
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| Department |
Department of Biology
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| Lab |
Brian Gregory
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| Street address |
433 S University Ave
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19103 |
| Country |
USA |
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| Platform ID |
GPL17639 |
| Series (1) |
| GSE94075 |
The Arabidopsis DNA methylome is relatively impervious to abiotic stress |
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| Relations |
| BioSample |
SAMN06274971 |
| SRA |
SRX2521074 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2468308_Drought-r3_CG.bed.bismark.cov.gz |
30.7 Mb |
(ftp)(http) |
COV |
| GSM2468308_Drought-r3_CG.bed.gz |
28.3 Mb |
(ftp)(http) |
BED |
| GSM2468308_Drought-r3_CG_100bp.bed.gz |
8.3 Mb |
(ftp)(http) |
BED |
| GSM2468308_Drought-r3_CHG.bed.bismark.cov.gz |
33.7 Mb |
(ftp)(http) |
COV |
| GSM2468308_Drought-r3_CHG.bed.gz |
31.5 Mb |
(ftp)(http) |
BED |
| GSM2468308_Drought-r3_CHG_100bp.bed.gz |
8.6 Mb |
(ftp)(http) |
BED |
| GSM2468308_Drought-r3_CHH.bed.bismark.cov.gz |
157.0 Mb |
(ftp)(http) |
COV |
| GSM2468308_Drought-r3_CHH.bed.gz |
157.3 Mb |
(ftp)(http) |
BED |
| GSM2468308_Drought-r3_CHH_100bp.bed.gz |
10.9 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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