SMED30022240

Overview
NameSMED30022240
Smed IDSMED30022240
Length (bp)300
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30022240 (SMED30022240) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022240 (SMED30022240) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30022240 (SMED30022240) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022240 (SMED30022240) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Alignments
SMED30022240 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.010054:8600..8880 +610
v31.039512:955..1236 +609
Homology
BLAST of SMED30022240 vs. Planmine SMEST
Match: SMESG000063550.1 (SMESG000063550.1)

HSP 1 Score: 76.6406 bits (187), Expect = 1.040e-17
Identity = 37/39 (94.87%), Postives = 37/39 (94.87%), Query Frame = -3
Query:   17 IVEVIRPFLYGKTRYAEKLKELMRKLGRELREARVELAQ 133
            IVEVIRPFLYGKTRYAEKLKELMRKLGRE REARVEL Q
Sbjct:  468 IVEVIRPFLYGKTRYAEKLKELMRKLGREFREARVELKQ 506          
BLAST of SMED30022240 vs. Planmine SMEST
Match: SMESG000080881.1 (SMESG000080881.1)

HSP 1 Score: 60.8474 bits (146), Expect = 4.379e-12
Identity = 26/37 (70.27%), Postives = 32/37 (86.49%), Query Frame = -3
Query:   23 IVEVIRPFLYGKTRYAEKLKELMRKLGRELREARVEL 133
            IV++IRP+LY K+RY EKLK LMR+ GRELRE R+EL
Sbjct: 2102 IVDIIRPYLYDKSRYGEKLKCLMRRFGRELRETRMEL 2138          
BLAST of SMED30022240 vs. Planmine SMEST
Match: SMESG000034473.1 (SMESG000034473.1)

HSP 1 Score: 60.077 bits (144), Expect = 8.243e-12
Identity = 26/37 (70.27%), Postives = 34/37 (91.89%), Query Frame = -3
Query:   23 IVEVIRPFLYGKTRYAEKLKELMRKLGRELREARVEL 133
            IV+ IRP+LY K+RY+EKLK+++RK+G ELREARVEL
Sbjct:  491 IVDCIRPYLYDKSRYSEKLKKMLRKMGHELREARVEL 527          
BLAST of SMED30022240 vs. Planmine SMEST
Match: SMESG000034473.1 (SMESG000034473.1)

HSP 1 Score: 59.6918 bits (143), Expect = 1.035e-11
Identity = 26/37 (70.27%), Postives = 34/37 (91.89%), Query Frame = -3
Query:   23 IVEVIRPFLYGKTRYAEKLKELMRKLGRELREARVEL 133
            IV+ IRP+LY K+RY+EKLK+++RK+G ELREARVEL
Sbjct:  183 IVDCIRPYLYDKSRYSEKLKKMLRKMGHELREARVEL 219          
BLAST of SMED30022240 vs. Planmine SMEST
Match: SMESG000057446.1 (SMESG000057446.1)

HSP 1 Score: 58.9214 bits (141), Expect = 1.987e-11
Identity = 26/37 (70.27%), Postives = 31/37 (83.78%), Query Frame = -3
Query:   23 IVEVIRPFLYGKTRYAEKLKELMRKLGRELREARVEL 133
            IV +IRP+LY K+RY EKLK LMR+ GRELRE R+EL
Sbjct:  664 IVNIIRPYLYDKSRYGEKLKCLMRRFGRELRETRMEL 700          
The following BLAST results are available for this feature:
BLAST of SMED30022240 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022240 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000063550.11.040e-1794.87SMESG000063550.1[more]
SMESG000080881.14.379e-1270.27SMESG000080881.1[more]
SMESG000034473.18.243e-1270.27SMESG000034473.1[more]
SMESG000034473.11.035e-1170.27SMESG000034473.1[more]
SMESG000057446.11.987e-1170.27SMESG000057446.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022240 ID=SMED30022240|Name=SMED30022240|organism=Schmidtea mediterranea sexual|type=transcript|length=300bp
GAATTTTATACCAACATTGTGCTAATTCAACTCTAGCCTCTCTCAACTCT
CTGCCCAATTTCCTCATTAATTCTTTCAACTTTTCAGCATATCTAGTTTT
TCCATACAAAAATGGTCGTATCACCTCTACAATCTCCAATTTACTTTCTG
TTTCCAATTCCGATTCCTCAAGTAGTTCTAATTTTTTATTGCCTCTTCTA
ATGGCATCTGCATCTTCTTGAGCAGAGTTACTTCCACTTTGCATCTTAAT
ACCACACACTTTTCCGGCCACAATTGCTACATATTCTGCGTCGATAAATA
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protein sequence of SMED30022240-orf-1

>SMED30022240-orf-1 ID=SMED30022240-orf-1|Name=SMED30022240-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=99bp
FIDAEYVAIVAGKVCGIKMQSGSNSAQEDADAIRRGNKKLELLEESELET
ESKLEIVEVIRPFLYGKTRYAEKLKELMRKLGRELREARVELAQCWYKI
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland