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| Status |
Public on Jun 06, 2019 |
| Title |
Comprehensive integration of single-cell data |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Single-cell transcriptomics (scRNA-seq) has transformed our ability to discover and annotate cell types and states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, including high-dimensional immunophenotypes, chromatin accessibility, and spatial positioning, a key analytical challenge is to integrate these datasets into a harmonized atlas that can be used to better understand cellular identity and function. Here, we developed a computational strategy to "anchor" diverse datasets together, enabling us to integrate and compare single-cell measurements not only across scRNA-seq technologies, but different modalities as well. As one demonstration of the method, we anchor single-cell protein measurements with a human bone marrow atlas to annotate and characterize lymphocyte populations. The multimodal data, generated using CITE-seq, is provided here alongside a corresponding bulk validation experiment.
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| Overall design |
Human PBMCs were profiled using CITE-seq and bulk RNA-seq.
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| Contributor(s) |
Butler A, Stuart T |
| Citation(s) |
31178118 |
| Submission date |
Mar 20, 2019 |
| Last update date |
Jun 12, 2019 |
| Contact name |
Andrew Butler |
| E-mail(s) |
abutler@nygenome.org
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| Organization name |
New York Genome Center
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| Lab |
Satija Lab
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| Street address |
101 6th Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10013 |
| Country |
USA |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA528319 |
| SRA |
SRP188993 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE128639_MNC_ADT_Barcodes.csv.gz |
569 b |
(ftp)(http) |
CSV |
| GSE128639_MNC_BULK_RNA_SampleIndices.csv.gz |
195 b |
(ftp)(http) |
CSV |
| GSE128639_MNC_HTO_Barcodes.csv.gz |
259 b |
(ftp)(http) |
CSV |
| GSE128639_RAW.tar |
37.8 Mb |
(http)(custom) |
TAR (of TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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