Omics · study · 2026
Protocol for low-input whole-genome bisulfite sequencing in plants
Listed in NCBI GEO
DNA methylation profiling of rare plant samples is limited by the scarcity of input DNA.
Description
This protocol uses Arabidopsis to describe tissue cryo-milling, Proteinase K lysis, direct bisulfite conversion, post-bisulfite adapter tagging library construction with random priming and adapter ligation, and MethylStar-based alignment and methylation calling. Benchmarking libraries were prepared from 5 pg to 50 ng of leaf genomic DNA and compared with conventional 50-ng WGBS.
The series also includes five libraries prepared directly from independently dissected Arabidopsis shoot apical meristems, with one meristem per library, to validate the workflow in low-input plant tissue.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE338nnn/GSE338396 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE338396 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1494441 ncbi.nlm.nih.gov/bioproject/PRJNA1494441 ↗
project · from NCBI GEO
Topics
- Stated by source
- Arabidopsis thaliana · Methylation profiling by high throughput sequencing
- From keywords
- Life Sciences
- Inferred from text
- DNA methylation profiling 75% · Sequencing 75%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE338396 | 15 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:methylation-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[method].local:method:dna-methylation-profiling | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[organism].NCBITaxon:3702 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |