SMED30014887

Overview
NameSMED30014887
Smed IDSMED30014887
Length (bp)430
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 SMED30014887 (SMED30014887) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014887 (SMED30014887) 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 SMED30014887 (SMED30014887) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014887 (SMED30014887) 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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Anatomical Expression

PAGE et. al., 2020



SMED30014887

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 19

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30014887h1SMcG0022441 SmedASXL_002930SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30014887h1SMcG0022441 SmedASXL_000277SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
X1 cellSMED30014887h1SMcG0022441 SmedASXL_007182SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30014887h1SMcG0022441 SmedASXL_007183SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30014887h1SMcG0022441 SmedASXL_000277SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
cephalic gangliaSMED30014887h1SMcG0022441 dd_Smed_v4_19022_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30014887h1SMcG0022441 dd_Smed_v4_19022_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30014887h1SMcG0022441 dd_Smed_v4_21084_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014887h1SMcG0022441 Contig40637uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014887h1SMcG0022441 Contig40637newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30014887h1SMcG0022441 dd_Smed_v4_15248_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30014887h1SMcG0022441 dd_Smed_v4_15248_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30014887h1SMcG0022441 dd_Smed_v4_15248_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30014887h1SMcG0022441 dd_Smed_v4_15248_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30014887h1SMcG0022441 dd_Smed_v6_19022_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
zeta neoblastSMED30014887h1SMcG0022441 dd_Smed_v4_19022_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30014887h1SMcG0022441 dd_Smed_v4_21084_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30014887h1SMcG0022441 SMED_34045_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30014887h1SMcG0022441 SMED_34045_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30014887 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.021405:1872..2322 +1721
v31.021405:2457..2887 +1569
v31.021405:2175..2603 +1560
v31.021405:1646..2039 +550
Homology
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BLAST of SMED30014887 vs. Planmine SMEST
Match: SMESG000009948.1 (SMESG000009948.1)

HSP 1 Score: 137.887 bits (346), Expect = 2.203e-38
Identity = 110/127 (86.61%), Postives = 117/127 (92.13%), Query Frame = 1 
Query:   40 LLGERN-SEKHEEIKNLEIIINRKKTEIIEGKDXXXXXXXXXXXXXXXXXXXXXXXXXXXQKDKEINIKCMELEIVIDEKIKLENDLIRTKNEIVILGDLISERHEEIKNLEIKIDTNQREINGKED 417
            L  E+N +EKHE+IKNLE  I+ K+ EIIE +DKIK LEEKNKIIYEEL LKENLEE+IKQKDKEINIKCMELEIVIDEKIKLENDLIRTKNEIVILGDLISERHEEIKNLEIKIDTNQREINGKED
Sbjct:  818 LKSEKNEAEKHEKIKNLETKIDTKQREIIEKEDKIKKLEEKNKIIYEELKLKENLEEIIKQKDKEINIKCMELEIVIDEKIKLENDLIRTKNEIVILGDLISERHEEIKNLEIKIDTNQREINGKED 944

HSP 2 Score: 129.028 bits (323), Expect = 3.410e-35
Identity = 110/163 (67.48%), Postives = 128/163 (78.53%), Query Frame = 1 
Query:    1 LENDLIRSKNEIELLGERNSEKHEEIKNLEIIINRKKTEIIEGKDXXXXXXXXXXXXXXXXXXXXXXXXXXXQKDKEINIKCMELEIVIDEKIKLENDLIRTKNEIVILGD----------------------LISERHEEIKNLEIKIDTNQREINGKEDKI 423
            LENDLIRSKNEIELLGERNSEKHEEIKNLEIIINRKKTEIIEGKDKIKILEEKNKIIY ELILK NL+E+IKQKD+EINIKCMEL+I+ +EKIKLENDLIR+KNEIVILG+                       ++++ EEI NL++ I+  ++EI+   D I
Sbjct:  994 LENDLIRSKNEIELLGERNSEKHEEIKNLEIIINRKKTEIIEGKDKIKILEEKNKIIYGELILKGNLDEIIKQKDEEINIKCMELQIINEEKIKLENDLIRSKNEIVILGENNSVKIIELIDFHEKKQIESKGYLTKQVEEISNLKLLIEEKEQEISKNNDTI 1156

HSP 3 Score: 108.997 bits (271), Expect = 3.198e-28
Identity = 102/142 (71.83%), Postives = 119/142 (83.80%), Query Frame = 1 
Query:    1 LENDLIRSKNEIELLGERNSEKHEEIKNLEIIINRKKTEIIEGKDXXXXXXXXXXXXXXXXXXXXXXXXXXXQKDKEINIKCMELEIVIDEKIKLENDLIRTKNEIVILGDLISERHEEIKNLEIKIDTNQREINGKEDKIK 426
            LENDLIR+KNEI +LG+  SE+HEEIKNLEI I+  + EI   +DKIK +EEKNKIIYEELILKENLEEMIKQKDKEINIKCMEL+I  +EKIKLENDLIR+KNEI +LG+  SE+HEEIKNLEI I+  + EI   +DKIK
Sbjct:  900 LENDLIRTKNEIVILGDLISERHEEIKNLEIKIDTNQREINGKEDKIKKIEEKNKIIYEELILKENLEEMIKQKDKEINIKCMELQIENEEKIKLENDLIRSKNEIELLGERNSEKHEEIKNLEIIINRKKTEIIEGKDKIK 1041
[Close]
BLAST of SMED30014887 vs. Planmine SMEST
Match: SMESG000009948.1 (SMESG000009948.1)

HSP 1 Score: 137.887 bits (346), Expect = 2.312e-38
Identity = 110/127 (86.61%), Postives = 117/127 (92.13%), Query Frame = 1 
Query:   40 LLGERN-SEKHEEIKNLEIIINRKKTEIIEGKDXXXXXXXXXXXXXXXXXXXXXXXXXXXQKDKEINIKCMELEIVIDEKIKLENDLIRTKNEIVILGDLISERHEEIKNLEIKIDTNQREINGKED 417
            L  E+N +EKHE+IKNLE  I+ K+ EIIE +DKIK LEEKNKIIYEEL LKENLEE+IKQKDKEINIKCMELEIVIDEKIKLENDLIRTKNEIVILGDLISERHEEIKNLEIKIDTNQREINGKED
Sbjct:  816 LKSEKNEAEKHEKIKNLETKIDTKQREIIEKEDKIKKLEEKNKIIYEELKLKENLEEIIKQKDKEINIKCMELEIVIDEKIKLENDLIRTKNEIVILGDLISERHEEIKNLEIKIDTNQREINGKED 942

HSP 2 Score: 128.642 bits (322), Expect = 3.614e-35
Identity = 110/163 (67.48%), Postives = 128/163 (78.53%), Query Frame = 1 
Query:    1 LENDLIRSKNEIELLGERNSEKHEEIKNLEIIINRKKTEIIEGKDXXXXXXXXXXXXXXXXXXXXXXXXXXXQKDKEINIKCMELEIVIDEKIKLENDLIRTKNEIVILGD----------------------LISERHEEIKNLEIKIDTNQREINGKEDKI 423
            LENDLIRSKNEIELLGERNSEKHEEIKNLEIIINRKKTEIIEGKDKIKILEEKNKIIY ELILK NL+E+IKQKD+EINIKCMEL+I+ +EKIKLENDLIR+KNEIVILG+                       ++++ EEI NL++ I+  ++EI+   D I
Sbjct:  992 LENDLIRSKNEIELLGERNSEKHEEIKNLEIIINRKKTEIIEGKDKIKILEEKNKIIYGELILKGNLDEIIKQKDEEINIKCMELQIINEEKIKLENDLIRSKNEIVILGENNSVKIIELIDFHEKKQIESKGYLTKQVEEISNLKLLIEEKEQEISKNNDTI 1154

HSP 3 Score: 108.997 bits (271), Expect = 3.356e-28
Identity = 102/142 (71.83%), Postives = 119/142 (83.80%), Query Frame = 1 
Query:    1 LENDLIRSKNEIELLGERNSEKHEEIKNLEIIINRKKTEIIEGKDXXXXXXXXXXXXXXXXXXXXXXXXXXXQKDKEINIKCMELEIVIDEKIKLENDLIRTKNEIVILGDLISERHEEIKNLEIKIDTNQREINGKEDKIK 426
            LENDLIR+KNEI +LG+  SE+HEEIKNLEI I+  + EI   +DKIK +EEKNKIIYEELILKENLEEMIKQKDKEINIKCMEL+I  +EKIKLENDLIR+KNEI +LG+  SE+HEEIKNLEI I+  + EI   +DKIK
Sbjct:  898 LENDLIRTKNEIVILGDLISERHEEIKNLEIKIDTNQREINGKEDKIKKIEEKNKIIYEELILKENLEEMIKQKDKEINIKCMELQIENEEKIKLENDLIRSKNEIELLGERNSEKHEEIKNLEIIINRKKTEIIEGKDKIK 1039
The following BLAST results are available for this feature:
BLAST of SMED30014887 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 SMED30014887 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 SMED30014887 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 SMED30014887 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 SMED30014887 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 SMED30014887 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 SMED30014887 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 SMED30014887 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 SMED30014887 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 SMED30014887 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 SMED30014887 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 SMED30014887 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 SMED30014887 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 SMED30014887 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000009948.12.203e-3886.61SMESG000009948.1[more]
SMESG000009948.12.312e-3886.61SMESG000009948.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014887 ID=SMED30014887|Name=SMED30014887|organism=Schmidtea mediterranea sexual|type=transcript|length=430bp
TTGGAAAATGATTTAATCCGAAGCAAAAACGAAATAGAACTTCTGGGAGA
ACGGAATTCTGAAAAACATGAGGAAATAAAAAATCTCGAAATCATAATTA
ACAGAAAAAAAACGGAGATTATTGAGGGAAAAGATAAAATCAAAATATTA
GAAGAAAAGAATAAAATTATATATGAAGAATTAATATTAAAAGAAAATTT
GGAAGAAATGATAAAACAGAAAGATAAGGAGATAAATATAAAATGTATGG
AATTGGAAATTGTAATTGACGAAAAAATCAAATTGGAAAATGATTTAATC
CGAACCAAAAACGAAATAGTTATATTAGGAGATTTGATTTCGGAAAGACA
TGAGGAAATAAAAAATCTAGAAATCAAAATTGACACAAACCAAAGAGAAA
TTAATGGAAAAGAAGATAAAATCAAAAAAA
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protein sequence of SMED30014887-orf-1

>SMED30014887-orf-1 ID=SMED30014887-orf-1|Name=SMED30014887-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp
LENDLIRSKNEIELLGERNSEKHEEIKNLEIIINRKKTEIIEGKDKIKIL
EEKNKIIYEELILKENLEEMIKQKDKEINIKCMELEIVIDEKIKLENDLI
RTKNEIVILGDLISERHEEIKNLEIKIDTNQREINGKEDKIKK
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 19..53