Arabidopsis thaliana
ChIP-seq(1)(2), CAGE-seq(1), ONT DNA methylation calling(2) and ONT-DRS transcriptomes(2)
| Line | Reference | ChIP-seq (1)(2) | CAGE-seq (1) | ONT DNA methylation (2) | ONT-DRS transcriptomes (2) | |
|---|---|---|---|---|---|---|
| Col-0 (WT) | TAIR10 | Ser5P (rep1, rep2), Ser2P (rep1, rep2) (1) | Sense (+), Antisense (-) | CpG, CHG, CHH | DRS-Col-0 (ref AtRTD3), DRS-AtRTD3 | |
| met1 | TAIR10 | Ser5P (rep1, rep2), Ser2P (rep1, rep2) (1) | Sense (+), Antisense (-) | CpG, CHG, CHH | DRS-met1 | |
| ddm1 | TAIR10 | Ser5P (rep1, rep2), Ser2P (rep1, rep2) (1) | Sense (+), Antisense (-) | CpG, CHG, CHH | DRS-ddm1 | |
| suvh456 | TAIR10 | Ser5P (rep1, rep2), Ser2P (rep1, rep2) (1) | Sense (+), Antisense (-) | NA | DRS-suvh456 | |
| ibm1 | TAIR10 | Ser5P (rep1, rep2), Ser2P (rep1, rep2) (1) | Sense (+), Antisense (-) | NA | DRS-ibm1 | |
| ibm2 | TAIR10 | IBM2 (2) Ser5P (rep1, rep2), Ser2P (rep1, rep2) (2) |
Sense (+), Antisense (-) | NA | DRS-ibm2 | |
| edm2 | TAIR10 | EDM2 (2) Ser5P (rep1, rep2), Ser2P (rep1, rep2) (2) |
Sense (+), Antisense (-) | NA | DRS-edm2 | |
| pol4 | TAIR10 | NA | Sense (+), Antisense (-) | NA | NA | |
| pol5 | TAIR10 | NA | Sense (+), Antisense (-) | NA | NA |
Raw data can be downloaded from:
(1) DDBJ using the following accession numbers: DRA009134, DRA009847.
(2) ENA using the following accession numbers: PRJEB53880 (RNA PloII ChIP-Seq), PRJEB53877 (ChIP-Seq), PRJEB53882 (ONT DNA), PRJEB53881 (ONT-DRS) .
Citations:
(1) Le et al. (2020) "Epigenetic regulation of spurious transcription initiation in Arabidopsis." Nature communications
(2) Berthelier et al. (2022) "Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana." bioRxiv