|
| Status |
Public on Mar 25, 2024 |
| Title |
Input for H3K9me2 ChIP-seq in ddm1;rdr1;rdr2;rdr6 ATHILA-hp5 biol Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
background: Col0
chip antibody: none
genotype: ddm1;rdr1;rdr2;rdr6 ATHILA-hp5
treatment: crosslinking
|
| Treatment protocol |
Crosslinking with 1% FA followed by quencing with 0.125M Glycine
|
| Growth protocol |
Plants were grown on MS media for ChIPseq and on soil for ONT sequencing.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously described (Inagaki et al., 2017). Genomic DNA was extracted with Qiagen Dneasy Plant for ONT.
ChIP-seq libraries were made with NEBNext Ultra II DNA Library Prep Kit. ONT libraries were made with ONT SQK-NBD114.24 Ligation sequencing
ChIP-seq and direct methylation sequencing (WGS)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
For ChIPseq: Adapter trimming with cutadapt, mapping with Bowtie2 and bigwigs generated with Deeptools.
For ONT: Base calling was performed with dorado, reads were aligned with minimap2 and consensus methylation calls were produced with modkit. Methylaiton ratios were extracted with bedtools and converted to bigwigs with UCSC tools.
Assembly: ColCEN v1.2
Supplementary files format and content: For ChIPseq: Bigwig files representating log fold change of count per million IP/Input for each biological replicate or normalized coverage for Inputs.
Supplementary files format and content: For ONT: Bigwigs files of scaled methylation ratio [0-1] at each cytosine, with ratios on the negative strand being multiplied by -1. One file for each sequence context: CG (.cpg), CHG (.chg) and CHH (.chh).
|
| |
|
| Submission date |
Mar 24, 2024 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Robert A Martienssen |
| E-mail(s) |
martiens@cshl.edu
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Department |
Delbruck Bldg.
|
| Lab |
Martienssen
|
| Street address |
1 Bungtown Rd
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE132005 |
Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs |
|
| Relations |
| BioSample |
SAMN40594354 |
| SRA |
SRX24056811 |
