SMED30020821

Overview
NameSMED30020821
Smed IDSMED30020821
Length (bp)377
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 SMED30020821 (SMED30020821) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020821 (SMED30020821) 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 SMED30020821 (SMED30020821) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020821 (SMED30020821) 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
SMED30020821 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000125:8688..9172 -1831
v31.000125:9100..9601 -1380
v31.000125:9306..9726 -934
v31.000125:9420..9863 -444
Homology
[Close]
BLAST of SMED30020821 vs. Planmine SMEST
Match: SMESG000014298.1 (SMESG000014298.1)

HSP 1 Score: 186.037 bits (471), Expect = 1.660e-55
Identity = 109/147 (74.15%), Postives = 110/147 (74.83%), Query Frame = 1 
Query:    1 NFKDEGVDNSEKDNCHSKNEDNEEIYDKSAEDVESKVEMEEIKPVESFEKDNY------------------------------------HSDNEDIEYKKSDEEIDDNLKEVDNFEKDNCHSENEDIGYKESEEKIDDNFKDEVENF 333
            NFK+EGVDNSEKDN HSKNEDNEEIYDKSAEDVESKVEMEEIKPVESFEKDNY                                    HSDNEDIEYKKSDEEIDDNLKEVDNFEKDNCHSENEDIGYKESEEKIDDNFKDEVENF
Sbjct: 1844 NFKEEGVDNSEKDNRHSKNEDNEEIYDKSAEDVESKVEMEEIKPVESFEKDNYHSDNEDIEYKKSDIKESDEEIDDNLKEVDNFEKDNCHSDNEDIEYKKSDEEIDDNLKEVDNFEKDNCHSENEDIGYKESEEKIDDNFKDEVENF 1990

HSP 2 Score: 135.576 bits (340), Expect = 8.111e-38
Identity = 84/116 (72.41%), Postives = 94/116 (81.03%), Query Frame = 1 
Query:    7 KDEGVDNSEKDNCHSKNEDNEEIYDKSAEDVESKVEMEEIKPVESFEKDNYHSDNEDIEYKK-----SDEEIDDNLKE--VDNFEKDNCHSENEDIGYKESEEKIDDNFKDEVENF 333
            K + V++ EKD  HS+NEDN E Y K++EDVE KVEMEEIKPVESFEKD YHSDNEDIEYKK     SDEEIDDN KE  VDNFEKDNCHS+NEDI YK+S+E IDDN K EV+NF
Sbjct: 1701 KIKPVESFEKDYYHSENEDNGETYAKASEDVERKVEMEEIKPVESFEKDYYHSDNEDIEYKKSDIKESDEEIDDNFKEEIVDNFEKDNCHSDNEDIEYKKSDEVIDDNLK-EVDNF 1815

HSP 3 Score: 103.99 bits (258), Expect = 8.335e-27
Identity = 62/75 (82.67%), Postives = 67/75 (89.33%), Query Frame = 1 
Query:    1 NFKDEGVDNSEKDNCHSKNEDNEEIYDKSAEDVESKVEMEEIKPVESFEKDNYHSDNEDIEYKKSDEEIDDNLKE 225
            NFKDE V+N EKDN  S+N+DNEE YDKSAEDVESKVEMEEIKPVESFEKDNYHSDNEDIEYK+S+ EID N KE
Sbjct: 1982 NFKDE-VENFEKDNYDSENDDNEENYDKSAEDVESKVEMEEIKPVESFEKDNYHSDNEDIEYKESEAEIDHNFKE 2055

HSP 4 Score: 85.1149 bits (209), Expect = 4.090e-20
Identity = 76/161 (47.20%), Postives = 89/161 (55.28%), Query Frame = 1 
Query:    1 NFKDEGVDNSEKDNCHSKNEDNEEIYDKSAEDVESKVEMEEIKPVESFEKDNYHSDNEDIEYKKSD-----EEIDDNLKE----------------------------------------VDNFEKDNCHSENEDIGY-----KESEEKIDDNFKDEVENF 333
            NFK+E VDN EKDNCHS NED E  Y KS E ++     + +K V++FEKDN HSDNEDIEYKKSD     EEIDDN KE                                        V++FEKDN HS+NEDI Y     KES+E+IDDN K EV+NF
Sbjct: 1775 NFKEEIVDNFEKDNCHSDNEDIE--YKKSDEVID-----DNLKEVDNFEKDNCHSDNEDIEYKKSDIKESNEEIDDNFKEEGVDNSEKDNRHSKNEDNEEIYDKSAEDVESKVEMEEIKPVESFEKDNYHSDNEDIEYKKSDIKESDEEIDDNLK-EVDNF 1927

HSP 5 Score: 83.1889 bits (204), Expect = 1.515e-19
Identity = 65/142 (45.77%), Postives = 82/142 (57.75%), Query Frame = 1 
Query:   19 VDNSEKDNCHSKNEDNEEIYDKSAEDVESKVEMEEIKPVESFEKDNYHSDNEDIEYKKSDEEIDDN---------------------------------------LKEVDNFEKDNCHSENEDIGYKESEEKIDDNFKDEVE 327
            VDN EKDNCHS NED E  Y KS E+++     + +K V++FEKDN HS+NEDI YK+S+E+IDDN                                       +K V++FEKDN HS+NEDI YKESE +ID NFK+EVE
Sbjct: 1924 VDNFEKDNCHSDNEDIE--YKKSDEEID-----DNLKEVDNFEKDNCHSENEDIGYKESEEKIDDNFKDEVENFEKDNYDSENDDNEENYDKSAEDVESKVEMEEIKPVESFEKDNYHSDNEDIEYKESEAEIDHNFKEEVE 2058
The following BLAST results are available for this feature:
BLAST of SMED30020821 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 SMED30020821 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 SMED30020821 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 SMED30020821 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 SMED30020821 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 SMED30020821 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 SMED30020821 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 SMED30020821 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 SMED30020821 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 SMED30020821 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 SMED30020821 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 SMED30020821 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 SMED30020821 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 SMED30020821 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000014298.11.660e-5574.15SMESG000014298.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020821 ID=SMED30020821|Name=SMED30020821|organism=Schmidtea mediterranea sexual|type=transcript|length=377bp
AATTTCAAAGATGAAGGAGTAGACAATTCCGAAAAAGATAATTGCCATTC
CAAAAATGAAGACAATGAAGAGATTTATGATAAGTCGGCTGAAGATGTGG
AAAGTAAAGTCGAGATGGAAGAAATAAAACCTGTTGAAAGTTTCGAAAAA
GATAATTATCATTCTGATAATGAAGACATTGAATATAAAAAATCAGACGA
AGAAATAGATGATAATTTAAAAGAAGTAGATAATTTCGAAAAAGATAATT
GCCATTCTGAGAATGAAGACATTGGATATAAAGAATCAGAAGAAAAAATA
GATGATAATTTCAAGGATGAAGTAGAAAATTTCGAAAAAGATAATTACGA
TTCCGAAAATGACGACAATGAAGAGAA
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protein sequence of SMED30020821-orf-1

>SMED30020821-orf-1 ID=SMED30020821-orf-1|Name=SMED30020821-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
NFKDEGVDNSEKDNCHSKNEDNEEIYDKSAEDVESKVEMEEIKPVESFEK
DNYHSDNEDIEYKKSDEEIDDNLKEVDNFEKDNCHSENEDIGYKESEEKI
DDNFKDEVENFEKDNYDSENDDNEE
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000012neural progenitor cell
PLANA:0000019muscle progenitor cell
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000463cholinergic neuron
PLANA:0000464GABAergic neuron
PLANA:0000478pharynx musculature
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 62..82
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..125
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..112