O-glycan profiles of 21 acute myeloid leukemia cell lines

Complete 23-feature released O-glycan fractional-abundance matrix in 21 AML cell lines from Integrated N- and O-Glycomics of Acute Myeloid Leukemia (AML) Cell Lines.

Usage

glyhub_GPST000214_O_AML_CellLines(
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Format

A glyexp::GlycomicSE with 23 features and 21 observations. The abundance assay is in percent fractional abundance. rowData has no glycan_structure column because no feature has a supported structural annotation.

Source

GlycoPOST GPST000214. . Study: https://doi.org/10.3390/cells10113058. Repository: https://glycopost.glycosmos.org/entry/GPST000214. Quantitative source: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8616353/supplementaryFiles.

Arguments

kind: "curated" returns a data object; "raw" returns the path to a verified source archive. Raw archives are currently available for CPTAC.
cache_dir: Cache directory, defaulting to tools::R_user_dir("glyhub", "cache"). Set option glyhub.cache_dir to change the default.
refresh: Download the pinned resource again, even if cached.
offline: Prohibit downloads; require a verified local resource.

Details

Source assay is the complete individual-glycan block only; following glycan-feature/derived-trait rows are not molecular features. Author-imputed values of 0.01 replacing zeros are preserved exactly as published; this curation does not reverse or add imputation. Only actual quantitative zero values become NA. No renormalization is applied. One source profile column represents each cell line; biological/technical replicate status of the main table is not specified by its headers and is left unknown. The RSD_MOLM-14 sheet is retained as auxiliary variability data rather than appended: biological rep1 overlaps technical replicates, and N-glycan technical and biological panels have different feature denominators. Isomer suffixes are preserved without collapsing rows.

Counts follow the author legend: H=Hex, N=HexNAc, F=Fuc, S=NeuAc, P=phosphate, Su=sulfate. In typed composition, sulfate uses S and sialic acid uses NeuAc. Structures are not inferred from composition, retention order or mass.

Access

Use glyhub_load("glyhub_GPST000214_O_AML_CellLines") to load this dataset.