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Series GSE94820 Query DataSets for GSE94820
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
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.
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:; 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.
Contributor(s) Villani A
Citation(s) 28428369, 30405621
Submission date Feb 13, 2017
Last update date Mar 20, 2019
Contact name Nir Hacohen
Organization name Broad Institute
Lab Nir Hacohen
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (2384)
GSM2483594 pDC_P10_S73
GSM2483595 pDC_P10_S74
GSM2483596 pDC_P10_S75
BioProject PRJNA374527

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 is available on Series record

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