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| Status |
Public on Mar 15, 2023 |
| Title |
bisulf.10012.rep4 |
| Sample type |
SRA |
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| Source name |
leaves
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaves
developmental stage: 14-leaf-rosette
genotype: 10012
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| Treatment protocol |
no treatment
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| Growth protocol |
21 degrees Celcius, on soil, long-day conditions (16h light, 8h dark)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from the frozen leaf tissue (14-leaf rosettes) using Nuclear Mag Plant kit (Machery-Nagel)
100bp PE
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
CG.methylation.32_accessions.Araport11_PC_TE.genebody.txt
CG.methylation.32_accessions.Araport11_PC_TE.promoter.txt
CG.methylation.32_accessions.our_annotation.genebody.txt
CG.methylation.32_accessions.our_annotation.promoter.txt
CHG.methylation.32_accessions.Araport11_PC_TE.genebody.txt
CHG.methylation.32_accessions.Araport11_PC_TE.promoter.txt
CHG.methylation.32_accessions.our_annotation.genebody.txt
CHG.methylation.32_accessions.our_annotation.promoter.txt
CHH.methylation.32_accessions.Araport11_PC_TE.genebody.txt
CHH.methylation.32_accessions.Araport11_PC_TE.promoter.txt
CHH.methylation.32_accessions.our_annotation.genebody.txt
CHH.methylation.32_accessions.our_annotation.promoter.txt
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| Data processing |
raw data reads were trimmed and then the data was aligned to the TAIR10 genome exactly as described in doi: https://doi.org/10.1101/2022.12.04.519028.
Methylation was called exactly as described in doi: https://doi.org/10.1101/2022.12.04.519028.
The methylation level per locus for each context was determined by dividing the number of methylated reads by the total number of reads covering the cytosines in the CG, CHG or CHH context. Thus, the values of methylation of the locus were ranging from 0 to 1 and roughly correspond to the ratio of methylated to total cytosines in the locus (we did not take the average of the ratios for each cytosine to avoid high error rates caused by low read coverage).
Assembly: TAIR10
Supplementary files format and content: CG.methylation.32_accessions.Araport11_PC_TE.genebody.txt contains a table with CG methylation levels calculated over the full locus for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CG.methylation.32_accessions.Araport11_PC_TE.promoter.txt contains a table with CG methylation levels calculated over promoter (TSS+/-200bp) for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CG.methylation.32_accessions.our_annotation.genebody.txt contains a table with CG methylation levels calculated over the full locus for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample
Supplementary files format and content: CG.methylation.32_accessions.our_annotation.promoter.txt contains a table with CG methylation levels calculated over the promoter (TSS+/-200bp) for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample
Supplementary files format and content: CHG.methylation.32_accessions.Araport11_PC_TE.genebody.txt contains a table with CHG methylation levels calculated over the full locus for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CHG.methylation.32_accessions.Araport11_PC_TE.promoter.txt contains a table with CHG methylation levels calculated over the promoter (TSS+/-200bp) for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CHG.methylation.32_accessions.our_annotation.genebody.txt contains a table with CHG methylation levels calculated over the full locus for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample
Supplementary files format and content: CHG.methylation.32_accessions.our_annotation.promoter.txt contains a table with CHG methylation levels calculated over the promoter (TSS+/-200bp) for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample
Supplementary files format and content: CHH.methylation.32_accessions.Araport11_PC_TE.genebody.txt contains a table with CHH methylation levels calculated over the full locus for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CHH.methylation.32_accessions.Araport11_PC_TE.promoter.txt contains a table with CHH methylation levels calculated over the promoter (TSS+/-200bp) for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CHH.methylation.32_accessions.our_annotation.genebody.txt contains a table with CHH methylation levels calculated over the full locus for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample
Supplementary files format and content: CHH.methylation.32_accessions.our_annotation.promoter.txt contains a table with CHH methylation levels calculated over the promoter (TSS+/-200bp) for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample
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| Submission date |
Mar 03, 2023 |
| Last update date |
Mar 15, 2023 |
| Contact name |
Aleksandra Kornienko |
| E-mail(s) |
kornienkoalexandra@gmail.com
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| Phone |
00431790449000
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| Organization name |
Gregor Mendel Institute
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| Lab |
Nordborg
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| Street address |
Dr. Bohrgasse 3
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| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL26208 |
| Series (2) |
| GSE224761 |
Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing |
| GSE226560 |
Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [Bisulfite-seq] |
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| Relations |
| BioSample |
SAMN33577143 |
| SRA |
SRX19556236 |
| 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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