3522a9acc8256a35230b07f2e7ab3fc08c827f33 mspeir Sat Sep 5 17:19:20 2026 -0700 singleCellSignalsPeaks: correct the hg38 description page counts and cite BrainVar, refs #38219 From the v503 code review. Commit 3aac3982aa2 dropped 5 hg38 subtracks and updated the makeDoc, but the dataset list on the description page was missed, so the page disagreed with both the .ra and the facet menu: - Risk Loci in Alzheimer's and Parkinson's: 1 peak subtrack, not 2 (neuro-degen-atac/peaks.bb was the one dropped) - BrainVar: 9 signal subtracks, not 13, and the text still described tracks "for all nuclei together" -- the 4 combined-stage tracks are exactly the ones dropped, so every remaining BrainVar track carries a life stage Counts re-derived from the .ra by type (bigWig = signal, else peak): the other 7 hg38 datasets and all 9 mm10 datasets were already right, 929 and 587 total. BrainVar was also the only hg38 dataset with no citation, while its methods text had grown quite specific. It now cites Werling et al. 2020, which described the cohort, with the caveat that the single-nucleus data shown here were not part of that paper -- the same distinction the Cell Browser desc.conf makes. Citing it bare would credit a bulk RNA-seq and WGS study for 10x Multiome data. References are alphabetical, so hg38 is now 10 and mm10 still 7. copySingleCellSignalsPeaksFiles.py: colors_json() reads the palette in a with block, and a malformed R,G,B row now raises the SystemExit the rest of the file uses, naming the file, line number and offending field, instead of a bare ValueError or TypeError from int() or the %02X format. Output is unchanged. makeDoc: the mm10 cell-class note now records that the bare "Progenitor" row in celltype-class.tsv is live rather than leftover -- build_stanzas' class_key() collapses plurals, so BrainVar's "Progenitors" looks up under the singular key and takes its class and color from that one row. Retiring or qualifying the row would grey out that track. A non-neural label needs a specific cell type added instead, which is how "Nephron progenitors" comes out Stromal. Also fixed a contradiction there: the file claimed celltype-class.tsv is built by build_celltype_crosswalks.py a hundred lines above the note saying, correctly, that it is hand-curated and not generated. The submitters confirmed BrainVar is 100 bp tiles, so the 1 kb in their methods text is an error and the page is right; recorded in the hg38 makeDoc. Co-Authored-By: Claude Opus 5 (1M context) diff --git src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html index b32c0c681fa..b6a12c180b0 100644 --- src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html +++ src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html @@ -20,56 +20,59 @@

Cortex ATAC: single-cell epigenomes of the developing human brain and cortical organoids. 12 signal and 69 peak subtracks (Ziffra et al. 2021).

Human and Mouse Retina Cell Atlas: accessibility across retinal cell types. 39 signal and 30 peak subtracks (Li et al. 2023, preprint).

Risk Loci in Alzheimer's and Parkinson's: accessibility across six adult human brain regions, with 359,022 cell type-specific regulatory elements used to interpret disease-associated - variants. 64 signal and 2 peak subtracks (Corces et al. 2020). + variants. 64 signal and 1 peak subtrack (Corces et al. 2020).

Multiomic Human Heart: accessibility across human cardiac development, aging, and disease, paired with expression data. 40 signal subtracks (Gao et al. 2026).

Human Cardiogenesis: accessibility of human fetal hearts at three early developmental stages, used to prioritize noncoding variants in congenital heart disease. 19 signal subtracks (Ameen et al. 2022).

Oligodendrocytes in Mouse EAE Model of MS: accessibility in the oligodendrocyte lineage; the tracks here are the accessibility measured in oligodendroglia from adult human brain. 18 signal subtracks (Meijer et al. 2022).

BrainVar: gene-activity signal from 10x Multiome of human prefrontal cortex across 119 donors, sampling the frontal cerebral wall prenatally and the - dorsolateral prefrontal cortex postnatally. Tracks are given for all nuclei - together and for the prenatal and postnatal subsets separately; progenitors - are present in the prenatal subset only. 13 signal subtracks. + dorsolateral prefrontal cortex postnatally. Tracks are given separately for + the prenatal and postnatal subsets; progenitors are present in the prenatal + subset only. 9 signal subtracks. The BrainVar cohort was described by + Werling et al. 2020, which paired whole-genome sequencing with bulk RNA-seq + of the same developmental window; the single-nucleus data shown here extend + that resource to single-cell resolution and were not part of that paper.

SEA-AD Brain ATAC: chromatin accessibility per cell subclass across the spectrum of Alzheimer's disease neuropathological change, from middle temporal gyrus and prefrontal cortex. 184 signal subtracks (Gabitto et al. 2024; Hawrylycz et al. 2024).

Display Conventions and Configuration

This is a faceted collection, so the subtracks are chosen with filter menus rather than a long checkbox list. Use the facets on the track configuration page to narrow the subtracks by dataset, tissue, life stage, condition, data @@ -302,30 +305,41 @@ Integrated multi-omics single cell atlas of the human retina. bioRxiv. 2023 Nov 8.

Meijer M, Agirre E, Kabbe M, van Tuijn CA, Heskol A, Zheng C, Mendanha Falcão A, Bartosovic M, Kirby L, Calini D et al. Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility. Neuron. 2022 Apr 6;110(7):1193-1210.e13. PMID: 35093191; PMC: PMC9810341

+Werling DM, Pochareddy S, Choi J, An JY, Sheppard B, Peng M, Li Z, Dastmalchi C, Santpere G, Sousa +AMM et al. + +Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing +Human Prefrontal Cortex. +Cell Rep. 2020 Apr 7;31(1):107489. +PMID: 32268104; PMC: PMC7295160 +

Zhang K, Hocker JD, Miller M, Hou X, Chiou J, Poirion OB, Qiu Y, Li YE, Gaulton KJ, Wang A et al. A single-cell atlas of chromatin accessibility in the human genome. Cell. 2021 Nov 24;184(24):5985-6001.e19. PMID: 34774128; PMC: PMC8664161

Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC, Shin D et al. Single-cell epigenomics reveals mechanisms of human cortical development.