O-glycan profiles in CAL51 Golgi knockout cells

Complete O-glycan relative-abundance profiles from CAL51 control, GOLGA5 knockout and GOLGA8M knockout cells, investigating organelle-biogenesis interactions.

Usage

glyhub_GPST000271_O_CAL51(
  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 7 features and 15 observations. The abundance assay is in percent relative abundance. rowData has no glycan_structure column because no feature has a supported structural annotation.

Source

GlycoPOST GPST000271. Summary - O_glycans. Study: https://doi.org/10.1038/s41556-023-01297-4. Repository: https://glycopost.glycosmos.org/entry/GPST000271. Quantitative source: https://glycopost.glycosmos.org/data/GPST000271.1/Glycan_supplementary_table_N_O_glycan.xlsx.

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

Five source-numbered observations are provided for each of the three cell conditions. The source table does not explicitly establish biological versus technical replicate status. Chromatographic features with equal compositions remain separate; no cross-isomer collapse is performed. Source mass and monosaccharide-count annotations remain available. No glycan topology is inferred from composition.

Composition and retention-time-resolved feature labels are preserved; structure is not assigned.

Access

Use glyhub_load("glyhub_GPST000271_O_CAL51") to load this dataset.