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SRP098918
Mus musculus
12 Downloadable Samples
Illumina HiSeq 2500
Description
Comparing WT mice to a mouse model of mental retardation, this work identifies genes which display differences in ribosome-bound mRNAs, in hippocampus CA1 pyramidal cells. These genes products are potent functional components of neuronal plasticity and hippocampus-dependent memory. Overall design: Using a triple transgenic mouse line, we immunoprecipitated the HA-Rpl22 protein to isolate and sequence ribosome-associated mRNA in CA1 pyramidal cells. Pairwise comparison of wild type and Fmr1 KO mice defined a specific gene expression profile.
Publication Title
Cell Type-Specific mRNA Dysregulation in Hippocampal CA1 Pyramidal Neurons of the Fragile X Syndrome Mouse Model.
Sample Metadata Fields
Specimen part, Subject
View Samples- Danio rerio
- 246 Downloadable Samples
- NextSeq 500
Description
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).
Publication Title
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing.
Sample Metadata Fields
Specimen part, Subject
View Samples- Danio rerio
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
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).
Publication Title
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing.
Sample Metadata Fields
Specimen part, Subject
View Samples- Danio rerio
- 8 Downloadable Samples
- IlluminaHiSeq2500
Description
We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas. Overall design: Examination of gene expression in two different cell types
Publication Title
Ligand-activated BMP signaling inhibits cell differentiation and death to promote melanoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio, Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset.
Sample Metadata Fields
Specimen part, Cell line
View Samples