GEO series

Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility

GSE281238 Homo sapiens (human) Other 7 samples Submitted 2025/02/25 Platform GPL18573

At a glance

human · 7 samples

Organism: Homo sapiens (human)
Samples: 7 samples: 3 × sci_L3_HiC_yi vs 3 × sci_L3_RNA/ATAC/DNA_yi261Groups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI.
Paper: Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibilityNucleic acids research · 2025

Summary (written by the submitters)

Single-cell combinatorial indexing (sci-) methods have addressed major limitations of throughput and cost for many single cell modalities. With the incorporation of linear amplification and 3-level barcoding in our suite of methods called sci-L3, we further addressed the limitations of uniformity in single cell genome amplification. Here, we build on the generalizability of sci-L3 by extending it to template strand sequencing (sci-L3-Strand-seq), genome conformation capture (sci-L3-Hi-C), and the joint profiling of RNA and chromatin accessibility (sci-L3-RNA/ATAC).

Read the full summary ↓

We demonstrate the ease of adapting sci-L3 to these new modalities by only requiring a single-step modification of the original protocol. As a proof-of-principle, we show our ability to detect sister chromatid exchanges, genome compartmentalization, and cell state specific features in thousands of single cells. We anticipate sci-L3 to be compatible with additional modalities, including DNA methylation (sci-MET) and chromatin associated factors (CUT&Tag), and ultimately enable a multi-omics readout of them.

Published in

Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility

Chovanec P, Yin Y · Nucleic acids research 2025 · PMID 39997216 · doi:10.1093/nar/gkaf101

This dataset

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Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE281238_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1182789. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39997216) ↗

Study design

3 × sci_L3_HiC_yi vs 3 × sci_L3_RNA/ATAC/DNA_yi261

Supports a between-group comparison across 6 samples.

How we read this: 2 replicated groups read from 7 sample titles; they account for 6 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8615493 sci_L3_HiC_yi237 sci_L3_HiC_yi
GSM8615494 sci_L3_HiC_yi238 sci_L3_HiC_yi
GSM8615495 sci_L3_HiC_yi239 sci_L3_HiC_yi
GSM8615496 sci_L3_RNA/ATAC/DNA_yi261_1 sci_L3_RNA/ATAC/DNA_yi2…
GSM8615497 sci_L3_RNA/ATAC/DNA_yi261_2 sci_L3_RNA/ATAC/DNA_yi2…
GSM8615498 sci_L3_RNA/ATAC/DNA_yi261_3 sci_L3_RNA/ATAC/DNA_yi2…
GSM8615499 sci_L3_Strand_seq_yi293

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