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Series GSE100911 Query DataSets for GSE100911
Status Public on Aug 04, 2017
Title Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart-seq]
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Summary Recent advances in single-cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here, we utilized massively parallel single-cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow, constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally-distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner, our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs, il2rgaY91fs and double homozygous mutant fish, identifying blood cell losses in T, B, and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells, classically-defined and erythroid-primed hematopoietic stem and progenitor cells, mucin secreting kidney cells, and kidney stem/progenitor cells. In total, our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish.
 
Overall design The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly, we performed single-cell RNA sequencing by a modified Smart-seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines, which label distinct blood cell types (n = 246 cells total). Secondly, we utilized droplet-based single-cell RNA sequencing (inDrop) to investigate unmarked, comprehensive hematopoietic lineage structure within wild-type, casper-strain zebrafish (N=3 animals, n=3,782 cells total). From this, we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly, we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild-type fish with mutant zebrafish with known immunodeficiencies, including prkdc(D3612fs) (N=3 animals, n=3,201 cells), il2rga(Y91fs) (N=2 animals, n=2,068 cells) and prkdc(D3612fs), il2rga(Y91fs) double compound mutant fish (N=2 animals, n=2,276 cells). Lastly, we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow (n=1,699 kidney cells).
 
Contributor(s) Tang Q, Langenau D
Citation(s) 28878000
Submission date Jul 07, 2017
Last update date Feb 18, 2019
Contact name Sowmya Iyer
E-mail sowmya.iyer@mgh.harvard.edu
Organization name Massachusetts General Hospital
Department Pathology
Street address 149 13th St
City Boston
State/province MA
ZIP/Postal code 02129
Country USA
 
Platforms (1)
GPL20828 Illumina NextSeq 500 (Danio rerio)
Samples (246)
GSM2696105 cd41_GFPlow.P3.A01
GSM2696106 cd41_GFPlow.P3.A02
GSM2696107 cd41_GFPlow.P3.A03
This SubSeries is part of SuperSeries:
GSE100913 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing
Relations
BioProject PRJNA393431
SRA SRP111340

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
GSE100911_SMARTseq_cell_data.txt.gz 2.3 Kb (ftp)(http) TXT
GSE100911_SMARTseq_counts.txt.gz 1.1 Mb (ftp)(http) TXT
GSE100911_SMARTseq_mapping_metrics.txt.gz 9.6 Kb (ftp)(http) TXT
Raw data are available in SRA
Processed data is available on Series record

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