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| Status |
Public on Apr 21, 2017 |
| Title |
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes and progenitors |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Peripheral blood mononuclear cells (PBMCs) were isolated from fresh blood using Ficoll-Paque density gradient centrifugation. Single-cell suspensions were stained with different antibody cocktails designed to enrich for particular immune cell populations, which were then single cell sorted in 96-well plates. Single cell RNA-sequencing libraries were subsequently generated for 2422 single cells using Smart-Seq2 (Picelli et al., Nature Methods, 2014). Cells were sequenced at a depth of 1-2M reads/cell.
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| Overall design |
The study was divided into two stages: (1) an exploratory phase, where 1140 single human blood dendritic cells and monocytes were profiled and 12 population samples; (2) a deep characterization phase, where an additional 1261 single cells and 9 population samples were profiled as part of follow-up studies. A total of 2422 single cell and population samples were processed using Smart-Seq2 protocol (Picelli et al., Nature Methods, 2014), which allows for the generation of full-length single cell cDNA, and sequencing libraries were generated using Illumina Nextera XT DNA library preparation kit.
Please note that [1] the raw data have been submitted to dbGaP (which has controlled access mechanisms at: http://www.ncbi.nlm.nih.gov/gap; phs001294.v1.p1) due to potential privacy concerns. Please contact the submitter or dbGaP to request access to controlled-access datasets.
[2] a few samples (38) were profiled but excluded from the processed data file since they were either a bulk sample (21) or excluded due to QC (17). Therefore, there are 1,140 and 1,244 data columns in two processed data files respectively, corresponding to total 2384 samples described in the records.
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| Contributor(s) |
Villani A |
| Citation(s) |
28428369, 30405621 |
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| Submission date |
Feb 13, 2017 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Nir Hacohen |
| Organization name |
Broad Institute
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| Lab |
Nir Hacohen
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (2384)
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| Relations |
| BioProject |
PRJNA374527 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE94820_raw.expMatrix_DCnMono.discovery.set.submission.txt.gz |
16.7 Mb |
(ftp)(http) |
TXT |
| GSE94820_raw.expMatrix_deeper.characterization.set.submission.txt.gz |
15.9 Mb |
(ftp)(http) |
TXT |
| Raw data provided as supplementary file |
| Processed data are available on Series record |
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