HCA Data Explorer

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics.

Updated August 30, 2022

Single-nucleus RNA-seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate or are frozen, and opens the way to human genetics studies, clinical trials, and precise cell atlases of large organs. However, such applications are currently limited by batch effects, processing, and costs. Here, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter recovered profiles. We develop DemuxEM, a computational tool that detects inter-sample multiplets and assigns singlets to their sample of origin, and validate its accuracy using sex-specific gene expression, species-mixing and natural genetic variation. Our approach will facilitate tissue atlases of isogenic model organisms or from multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.

Jellert T GaublommeBroad Institute of Harvard and MITjellert.gaublomme@columbia.edu
Orit Rozenblatt-RosenBroad Institute of Harvard and MITorit@broadinstitute.org
Aviv RegevBroad Institute of Harvard and MIT,aregev@broadinstitute.org
Jellert T Gaublomme1
Bo Li2
Cristin McCabe1
Abigail Knecht1
Yiming Yang3
Eugene Drokhlyansky1
Nicholas Van Wittenberghe1
Julia Waldman1
Danielle Dionne1
Lan Nguyen1
Philip L De Jager4
Bertrand Yeung5
Xinfang Zhao5
Naomi Habib1
Orit Rozenblatt-Rosen1
Aviv Regev2
1Broad Institute of Harvard and MIT
2Broad Institute of Harvard and MIT,
3Massachusetts General Hospital and Harvard Medical School
4Columbia University Medical Center
5BioLegend Inc.
Wei Kheng Teh

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/dc1a41f6-9e09-42a6-959e-3be23db6da56

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

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Analysis Portals

None

Project Label

NucleiMultiplexHashing

Species

2 species

Sample Type

specimens

Anatomical Entity

brain

Organ Part

2 organ parts

Selected Cell Types

Unspecified

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

2 development stages

Library Construction Method

10x v2 3'

Nucleic Acid Source

single nucleus

Paired End

false

Analysis Protocol

PCA_analysis, snRNAseq_data_analysis

File Format

5 file formats

Cell Count Estimate

6.1k

Donor Count

22
fastq15 file(s)mtx4 file(s)tsv8 file(s)txt13 file(s)xlsx1 file(s)