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| Status |
Public on Mar 15, 2023 |
| Title |
1254.rep2.H3K4me3 |
| Sample type |
SRA |
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| Source name |
leaves (developmental stage: 14-leaf-rosette)
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaves (developmental stage: 14-leaf-rosette)
genotype: 1254
treatment: H3K4me3
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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 isolation using Qiagen PCR purification kit Qiaquick with 0.3M Sodium Acetate
ChIP-seq libraries were prepared from a half of the resulting DNA sample (due to very low amounts we did not measure the DNA concentrations) with the NEBNext Ultra II DNA kit (New England Biolabs) according to the manufacturer’s protocol
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
100bp SE
chip.5marks.14accessions.Araport11_PCs_TEs.log2_input_normalized_coverage.80_20_quantiles_normalized.genebody.bed
chip.5marks.14accessions.Araport11_PCs_TEs.log2_input_normalized_coverage.genebody.bed
chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.80_20_quantiles_normalized.genebody.bed
chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.80_20_quantiles_normalized.promoter.bed
chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.genebody.bed
chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.promoter.bed
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| Data processing |
Raw ChIP-seq reads were mapped using STAR with the following options --alignIntronMax 5 --outFilterMismatchNmax 10 --outFilterMultimapNmax 1 --alignEndsType EndToEnd. Only samples with >1mln unique non-duplicated reads were used for the analysis.
Aligned BAM files from each ChIP-sample were then normalized by the corresponding input samples using bamCompare from deeptools with the following options: --operation log2 --ignoreDuplicates --effectiveGenomeSize 119481543 and bigwig and bedgraph files were created.
Read coverage over loci and promoters was estimated using bedtools map on the bedgraph files with the “mean” operation.
To estimate the variation of the histone modification levels, the chip-seq coverage values were normalized again to achieve the same range of values across accessions. For this we applied a quantile normalization, setting the 20%- and 80%-quantile values for each sample to the same value with the function in R: quantile_minmax <- function(x) {(x-quantile(x,.20)) / (quantile(x,.80) - quantile(x,.20))}.
the processed data files contain input-normalized (or input and quantile normalized) ChIP-seq coverage values averaged across replicates for each accession/histone mark. Most accessions/marks had 2 replicates, but some are completely missing and some only have 1 replicate because we did not manage to get enough unique-non-duplicated reads (>1mln) in those data samples, or there was another quality problem with the data samples such as potential contamination: such samples were exculded, were not used for the analyses and are not submitted as part of this dataset.
Assembly: TAIR10
Supplementary files format and content: chip.5marks.14accessions.Araport11_PCs_TEs.log2_input_normalized_coverage.80_20_quantiles_normalized.genebody.bed is a table with ChIP seq coverage for up to 5 histone marks in 14 accessions, input normalized calculated over the whole locus and quantile normalized. Araport PC genes and TEs. replicates were averaged for each accession/antibody
Supplementary files format and content: chip.5marks.14accessions.Araport11_PCs_TEs.log2_input_normalized_coverage.genebody.bed is a table with ChIP seq coverage for up to 5 histone marks in 14 accessions, input normalized calculated over the whole locus. Araport PC genes and TEs.
Supplementary files format and content: chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.80_20_quantiles_normalized.genebody.bed is a table with ChIP seq coveragefor up to 5 histone marks in 14 accessions, input normalized calculated over the whole locus and quantile normalized. Annotation of 5 gene types produced in this study
Supplementary files format and content: chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.80_20_quantiles_normalized.promoter.bed is a table with ChIP seq coverage for up to 5 histone marks in 14 accessions, input normalized calculated overpromoters (TSS+/-200bp)and quantile normalized. Annotation of 5 gene types produced in this study
Supplementary files format and content: chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.genebody.bed is a table with ChIP seq coverage for up to 5 histone marks in 14 accessions, input normalized calculated over the whole locus. Annotation of 5 gene types produced in this study
Supplementary files format and content: chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.promoter.bed is a table with ChIP seq coverage for up to 5 histone marks in 14 accessions, input normalized, calculated over promoters (TSS+/- 200bp). Annotation of 5 gene types produced in this study
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| Submission date |
Mar 06, 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 |
| GSE226682 |
Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [ChIP-Seq] |
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| Relations |
| BioSample |
SAMN33593873 |
| SRA |
SRX19568019 |
| 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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