UCLA IGVF Consortium
Preprint in preparation · IGVF Consortium · UCLA

Epigenomic heterogeneity and spatial organization during human reprogramming

Terence W. Li1,2,3,*, Justin Langerman4,*, Cuining Liu1,3,*, Yu Sun4,*, Mohammad S. Baig1,5, Gianna Kim1, Jingyuan Fu4,6, Rayyan Irfan Ghoor1, Yi Zhang1, Zach Von Behren1, Min Jen Tsai1, Malina Elena Cantemir1, Kevin D. Abuhanna1,5, Edward Chen1, Jon Paino6, Gideon Shaked4, Lily Zhao4, Lisa Barooah4, Amy Sun4, Andrea Garcia Angulo4, Alexander Lee4, Sophia Peavy4, Eleazar Eskin1,2,6, Noah Zaitlen1,2,7, Brunilda Balliu2,8,9,†, Jason Ernst2,4,6,†, Chongyuan Luo1,†, Kathrin Plath4,†

Affiliations · *co-first authors · †co-corresponding authors
  1. Department of Human Genetics, David Geffen School of Medicine, UCLA
  2. Department of Computational Medicine, David Geffen School of Medicine, UCLA
  3. Bioinformatics Interdepartmental Program, UCLA
  4. Department of Biological Chemistry, David Geffen School of Medicine, UCLA
  5. Genetics and Genomics Graduate Program, UCLA
  6. Computer Science Department, Henry Samueli School of Engineering and Applied Science, UCLA
  7. Department of Neurology, David Geffen School of Medicine, UCLA
  8. Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA
  9. Department of Biostatistics, Fielding School of Public Health, UCLA
↓ Download the data ▤ Preprint ⬢ IGVF portal

Summary

the study

Fibroblasts from four individuals were reprogrammed to induced pluripotent stem cells and sampled at up to 11 time points. Cells were profiled for single-nucleus gene expression and chromatin accessibility (10x Multiome), DNA methylation with transcriptome (snmCT-seq), and DNA methylation with 3D genome organization (sn-m3C-seq). Highly multiplexed spatial transcriptomics (CosMx) was performed on selected time points, and each donor was whole-genome sequenced.

Get the data

Click a series of things to define a set: samples on the grid — C29 day 0, C29 day 1, … C37 day 0 — narrowed by modality, tier and file type on the left.

How the data is organised

three tiers, five modalities

Raw/processed data is deposited on the IGVF portal and publicly released. The five principal analysis sets below are post-QC, and we provide download links for all raw/intermediate files used to generate them.

Raw measurement sets — FASTQ + seqspec → Processed intermediate analysis sets — alignments, matrices, fragments → Analysis-ready principal analysis sets — final matrices + cell annotations

Analysis-ready files

final per-modality outputs · —

Grouped by file type, one click per file.

Processed and raw files, by type

whole-tier manifests

Each row gives you a manifest — a TSV with one row per file including its download URL, size and md5.