Omic and Multidimensional Spatial Atlas of Metastatic Breast Cancers

Written and checked by a reviewer, not generated from metadata.

1. 1. How does the spatial organization of a metastatic tumor change as it acquires resistance to therapy?

   Needs approved accessHUMAN

   Serial biopsies with multiplexed imaging and spatial transcriptomics on the same patients across treatment, with therapy and follow-up clinical components present. This longitudinal spatial design is essentially unique in public data.

   Statistical note: Patient numbers are small by design - deep serial sampling trades breadth for depth. Treat this as a case-series design with within-patient comparison, not a cohort study.

   NeedsMultiplexed tissue imagingSpatial transcriptomicsTreatment records

2. 2. Do single-cell chromatin accessibility changes precede the transcriptional changes that accompany resistance?

   Needs approved accessHUMAN

   Single-cell ATAC and single-cell RNA on the same serial samples allow regulatory and transcriptional state to be ordered in time within a patient.

   NeedsSingle-cell ATAC sequencingSingle-cell RNA sequencing

3. 3. Can ultrastructural features from electron microscopy be related to molecular state measured on the same tissue?

   Needs approved accessHUMAN

   Electron microscopy appears in no other dataset in this corpus. Linking ultrastructure to spatial and single-cell molecular data on the same specimens is possible only here.

   Statistical note: Descriptive and mechanistic rather than statistically powered.

   NeedsElectron microscopyMultiplexed tissue imaging

4. 4. How do multiplexed imaging and spatial transcriptomics agree when applied to the same tissue section?

   Needs approved accessHUMAN

   Both assays are present on shared specimens, which makes cross-platform concordance measurable - a methodological question the spatial field needs answered and rarely can.

   NeedsMultiplexed tissue imagingSpatial transcriptomics

Written by a reviewer against the source, not inferred from what is missing.

Articles that analyzed these data, counted separately from articles that only cited the paper. Only the first counts as reuse.

Analyses someone ran on these data end to end, each with a receipt recording when it ran, against which packages and for how long.

Nobody has shared an analysis of this dataset yet. The examples on other datasets cover the common patterns and can be adapted - and if you adapt one, it belongs here.

Starter code generated from this record’s own identifiers, then the access steps.

import synapseclient

syn = synapseclient.login()          # uses ~/.synapseConfig or SYNAPSE_AUTH_TOKEN
for sid in ["syn35465046","syn39140594","syn39140863","syn39141309"]:
    entity = syn.get(sid, downloadLocation="./htan")
    print(sid, entity.name)
# Browse the atlas at https://humantumoratlas.org/explore

curl -s https://cd2s.vercel.app/data/datasets/htan-omic-and-multidimensional-spatial-atlas-of-metastatic-breast-cancers.json | python3 -c '
import json, sys
r = json.load(sys.stdin)
for l in r["limitations"]:
    print(l["severity"].upper(), "-", l["statement"][:120])
print("survival endpoint:", r["longitudinal"]["has_survival_endpoint"], "| treatment response:", r["longitudinal"]["has_treatment_response"])'

Access steps

1. 1

   Explore the atlas in the HTAN Data PortalFor people1 hour

   https://humantumoratlas.org/explore
2. 2

   Register with Synapse and accept the HTAN data use termsFor people1 day

   This unlocks the level 3 and 4 derived data and most imaging without a formal data access request.

   Requires: Synapse account

   https://humantumoratlas.org/data-access
3. 3

   Request dbGaP access only if you need level 1 or 2 sequence dataFor peopledays to a few weeks

   Requires: eRA Commons account, institutional signing official approval

   https://humantumoratlas.org/data-access
4. 4

   Give an agent a Synapse token, not a passwordFor agents

   Unauthenticated calls return metadata and no files, so an agent should report the credential requirement explicitly.

   Requires: SYNAPSE_AUTH_TOKEN

   export SYNAPSE_AUTH_TOKEN=...
   synapse get syn35465046

   https://help.synapse.org/docs/Getting-Started.2055471150.html

   Generated from repository policy. Check the linked policy before downloading.

All of it, and more, is in this record’s JSON.