Machine-readable copies of the manuscript supplementary tables that the data
download and analysis workflows depend on. See ../DATA.md for the
download recipes that use these, and the hdma agent skill
(../.claude/skills/hdma/references/data.md).
| file | table | what it is |
|---|---|---|
table_s14.tsv |
Table S14 | map of every deposited data type → Zenodo record/DOI (the download index) |
table_s2.tsv |
Table S2 | per-cluster cell metadata and the cluster-naming map |
table_s6.tsv |
Table S6 | motif lexicon / compendium annotations |
table_s14.tsv — Table S14 (data deposition index)The authoritative map used by the download recipes. One row per deposition; most data types span several “Part” depositions.
| column | description |
|---|---|
data_type |
kind of data (filter on this to select a product) |
size |
download size of the deposition |
depo_name |
human-readable Zenodo deposition name |
record_id |
Zenodo record ID (feed to get_urls.py) |
url |
concept DOI (resolves to the latest version) |
table_s2.tsv — Table S2 (cell metadata / cluster map)One row per cluster. The compartment (col 5) and Cluster_ChromBPNet (col 19)
columns drive the cell-type download recipes.
| column | description |
|---|---|
Cluster |
unique cluster id |
organ |
organ name |
organ_code |
abbreviated organ name |
cluster_id |
cluster id within organ |
compartment |
cellular compartment (epithelial/endothelial/immune/stromal) |
L1_annot |
level 1 cell type annotation (n=203) |
L2_annot |
level 2 cell type annotation (n=134) |
L3_annot |
level 3 cell type annotation (n=37) |
dend_order |
order of cluster from hierarchically clustering L1 cell types |
ncell |
number of cells in cluster |
median_numi |
median RNA number of UMIs per cell |
median_ngene |
median RNA number of genes per cell |
median_nfrags |
median ATAC number of fragments per cell |
median_tss |
median ATAC TSS enrichment ratio per cell |
median_frip |
median ATAC fraction of reads in peaks per cell |
note |
notes used for cell type annotation |
organ_color |
color for clusters based on organ |
compartment_color |
color for clusters based on compartment |
Cluster_ChromBPNet |
cluster id used in ChromBPNet models |
table_s6.tsv — Table S6 (motif lexicon / compendium)One row per compendium motif. merged_pattern maps a compendium motif back to
its per-cell-type constituent motifs.
| column | description |
|---|---|
idx_uniq |
unique index for the motif within the compendium |
motif_name |
unique motif name (prefix = idx_uniq, suffix = annotation) |
motif_name_safe |
computationally safe motif_name (no slashes or pipe) |
class |
motif contribution to accessibility (Activating or Repressive) |
total_instances_across_celltypes |
total motif instances across all 189 modeled cell types |
cwm_logo_fwd |
filename of the forward CWM logo PNG (see Table S14) |
cwm_logo_rev |
filename of the reverse CWM logo PNG (see Table S14) |
query_consensus |
consensus sequence for the trimmed CWM |
annotation |
granular motif annotation (<family>:<TF>#<index> or <family>:<subfamily>/<alt>#<index>, Vierstra v2.1 convention; composite constituents joined by underscores) |
annotation_broad |
broad motif annotation used to group motifs in analyses/figures |
category |
motif category (base, base_with_flanks, homocomposite, heterocomposite, partial, repeat, unresolved) |
best_match_TF |
TF associated with the best-matching known motif in databases (see Methods) |
best_match_motif |
best-matching known motif in databases |
best_match_TOMTOM_qval |
TOMTOM q-value for similarity to the best match |
best_match_TFs_in_family |
other TFs in the same family as best_match_TF (HOCOMOCO) |
best_match_TFs_in_Vierstra_archetype |
other TFs whose motifs share the Vierstra v2.1 cluster of the best match |
total_seqlets_across_celltypes |
total seqlets across all constituent motifs aggregated into this compendium motif |
merged_pattern |
name of the per-cell-type motif cluster corresponding to this compendium motif (maps back to constituents) |
n_constituent_motifs |
number of motifs aggregated into this compendium motif |
n_constituent_celltypes |
number of cell types contributing at least one constituent motif |
constituent_organs |
number of organs contributing at least one constituent motif |
constituent_celltypes |
L2_annot of the cell types contributing constituent motifs |