SMED30033360

Overview
NameSMED30033360
Smed IDSMED30033360
Length (bp)920
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 SMED30033360 (SMED30033360) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30033360 (SMED30033360) 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 SMED30033360 (SMED30033360) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30033360 (SMED30033360) 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




SMED30033360

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30033360h1SMcG0012660 SmedASXL_012345SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30033360h1SMcG0012660 SmedASXL_012345SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30033360h1SMcG0012660 dd_Smed_v4_12537_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30033360h1SMcG0012660 dd_Smed_v4_12537_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30033360h1SMcG0012660 SMED_13022_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30033360h1SMcG0012660 SMED_13022_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30033360h1SMcG0012660 SmWIOct06_036443GPL14150_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
SMED30033360 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000075:59835..61050 +4439
Homology
BLAST of SMED30033360 vs. TrEMBL
Match: A0A504YDL1 (TPX2 domain-containing protein OS=Fasciola gigantica OX=46835 GN=FGIG_01591 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 3.489e-6
Identity = 26/79 (32.91%), Postives = 51/79 (64.56%), Query Frame = 2
Query:  596 PPLSSYVKPKPATMPHSPKLSTEIRAKERNKYNMQLKERENQLKLKKQKEDETKMKDSSKKLEILRKNLIHKPEPIRKY 832
            PP    +  +   +P+ P+L+T  RA +R K++  L+ R + ++LK+Q  + ++  +  K+++ LR+ L+HKP+PIR+Y
Sbjct:   15 PPFVPQLSTRSPLVPNPPRLATSERAVQRLKFDEMLQRRRHSVELKQQAMEASRRAEEEKQVKRLRQELVHKPQPIRRY 93          
BLAST of SMED30033360 vs. TrEMBL
Match: A0A154P6R3 (Targeting protein for Xklp2 OS=Dufourea novaeangliae OX=178035 GN=WN55_08284 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 6.573e-6
Identity = 32/79 (40.51%), Postives = 48/79 (60.76%), Query Frame = 2
Query:  596 PPLSSYVKPKPATMPHSPKLSTEIRAKERNKYNMQLKERENQLKLKKQKEDETKMKDSSKKLEILRKNLIHKPEPIRKY 832
            PP       K ++ P +P L T IRA+ER +++  L+E+E Q + +  KE   K K+  K++ ILRK  +HK +PIRKY
Sbjct:  205 PPFIPCRTRKNSSRPKTPLLQTAIRAQERKRFDEILREKEIQRQQQSLKEIIVKQKEQEKEIAILRKQTVHKAQPIRKY 283          
BLAST of SMED30033360 vs. Planmine SMEST
Match: SMESG000074320.1 (SMESG000074320.1)

HSP 1 Score: 508.834 bits (1309), Expect = 0.000e+0
Identity = 251/252 (99.60%), Postives = 251/252 (99.60%), Query Frame = 2
Query:   83 MADCETKITGQDESIDEIVLICDNGFKQIESKKNTENEFLKKLSLTGFKNEKFGYDLDVNSQISSIQNIHLNDANLPKDHPKIRNKEHNGIPFKRTSRSAITQFHCNKENNSSTKDSVTYSLNKLKPLVVKKHNPSEVSAGYPKNINNNFRVPLSVKSNSTATSNQDTKIFPPLSSYVKPKPATMPHSPKLSTEIRAKERNKYNMQLKERENQLKLKKQKEDETKMKDSSKKLEILRKNLIHKPEPIRKYHP 838
            MADCETKITGQDESIDEIVLICDNGFKQIESKKNTENEFLKKLSLTGFKNEKFGYDLDVNSQISSIQNIHLNDANLPKDHPKIRNKEHNGIPFKRTSRSAITQFHCNKENNSSTKDSVTYSLNKLKPLVVKKHNPSEVS GYPKNINNNFRVPLSVKSNSTATSNQDTKIFPPLSSYVKPKPATMPHSPKLSTEIRAKERNKYNMQLKERENQLKLKKQKEDETKMKDSSKKLEILRKNLIHKPEPIRKYHP
Sbjct:    1 MADCETKITGQDESIDEIVLICDNGFKQIESKKNTENEFLKKLSLTGFKNEKFGYDLDVNSQISSIQNIHLNDANLPKDHPKIRNKEHNGIPFKRTSRSAITQFHCNKENNSSTKDSVTYSLNKLKPLVVKKHNPSEVSTGYPKNINNNFRVPLSVKSNSTATSNQDTKIFPPLSSYVKPKPATMPHSPKLSTEIRAKERNKYNMQLKERENQLKLKKQKEDETKMKDSSKKLEILRKNLIHKPEPIRKYHP 252          
BLAST of SMED30033360 vs. Planmine SMEST
Match: SMESG000074320.1 (SMESG000074320.1)

HSP 1 Score: 421.779 bits (1083), Expect = 6.915e-151
Identity = 209/210 (99.52%), Postives = 209/210 (99.52%), Query Frame = 2
Query:  209 LSLTGFKNEKFGYDLDVNSQISSIQNIHLNDANLPKDHPKIRNKEHNGIPFKRTSRSAITQFHCNKENNSSTKDSVTYSLNKLKPLVVKKHNPSEVSAGYPKNINNNFRVPLSVKSNSTATSNQDTKIFPPLSSYVKPKPATMPHSPKLSTEIRAKERNKYNMQLKERENQLKLKKQKEDETKMKDSSKKLEILRKNLIHKPEPIRKYHP 838
            LSLTGFKNEKFGYDLDVNSQISSIQNIHLNDANLPKDHPKIRNKEHNGIPFKRTSRSAITQFHCNKENNSSTKDSVTYSLNKLKPLVVKKHNPSEVS GYPKNINNNFRVPLSVKSNSTATSNQDTKIFPPLSSYVKPKPATMPHSPKLSTEIRAKERNKYNMQLKERENQLKLKKQKEDETKMKDSSKKLEILRKNLIHKPEPIRKYHP
Sbjct:    5 LSLTGFKNEKFGYDLDVNSQISSIQNIHLNDANLPKDHPKIRNKEHNGIPFKRTSRSAITQFHCNKENNSSTKDSVTYSLNKLKPLVVKKHNPSEVSTGYPKNINNNFRVPLSVKSNSTATSNQDTKIFPPLSSYVKPKPATMPHSPKLSTEIRAKERNKYNMQLKERENQLKLKKQKEDETKMKDSSKKLEILRKNLIHKPEPIRKYHP 214          
The following BLAST results are available for this feature:
BLAST of SMED30033360 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 SMED30033360 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 SMED30033360 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 SMED30033360 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 SMED30033360 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 SMED30033360 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 SMED30033360 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 SMED30033360 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A504YDL13.489e-632.91TPX2 domain-containing protein OS=Fasciola giganti... [more]
A0A154P6R36.573e-640.51Targeting protein for Xklp2 OS=Dufourea novaeangli... [more]
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BLAST of SMED30033360 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 SMED30033360 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 SMED30033360 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 SMED30033360 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 SMED30033360 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 SMED30033360 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000074320.10.000e+099.60SMESG000074320.1[more]
SMESG000074320.16.915e-15199.52SMESG000074320.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033360 ID=SMED30033360|Name=SMED30033360|organism=Schmidtea mediterranea sexual|type=transcript|length=920bp
ATTAAATGATACAAAGAAAGTAACATTGTTTTAATATTATTGTAAATCAT
TTCCAGTTTTATTTAATTTTCAATCTTTATTAATGGCTGATTGTGAAACA
AAAATAACTGGTCAAGACGAATCTATTGATGAAATAGTGCTGATTTGCGA
TAATGGATTCAAACAAATTGAATCTAAAAAAAATACAGAAAACGAATTTC
TCAAAAAATTATCTTTAACTGGGTTTAAAAATGAAAAATTCGGTTATGAT
TTAGACGTAAATAGTCAAATTAGCTCAATACAAAATATCCACTTGAATGA
TGCAAATTTACCAAAAGATCATCCTAAAATTAGGAATAAAGAGCACAATG
GAATTCCATTTAAAAGAACAAGTCGTTCTGCTATAACGCAATTTCATTGT
AACAAAGAAAATAATTCTAGTACTAAAGACAGTGTTACATATAGTCTTAA
TAAATTGAAGCCGTTAGTTGTTAAAAAACATAATCCATCTGAAGTTTCTG
CGGGATATCCTAAAAATATCAATAACAATTTTCGAGTTCCTCTTTCAGTC
AAATCAAATTCGACTGCTACAAGTAATCAAGATACGAAAATTTTTCCTCC
ATTATCAAGCTACGTAAAACCTAAACCGGCAACAATGCCGCATTCCCCGA
AATTGTCGACCGAAATTCGAGCTAAAGAGAGAAACAAATATAATATGCAA
TTAAAGGAAAGAGAGAACCAATTGAAGTTAAAAAAACAGAAAGAAGATGA
AACAAAAATGAAAGACTCATCAAAGAAATTGGAAATATTAAGAAAGAACC
TGATTCACAAACCTGAACCGATTAGGAAATACCATCCTTGAGTTGATCTA
TTTTGTTTCAGTTGTCGTTTTTTGTTTTGCAGTTAATAAATCATTTAATT
ATGACATTCGTTTTTTTTCT
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protein sequence of SMED30033360-orf-1

>SMED30033360-orf-1 ID=SMED30033360-orf-1|Name=SMED30033360-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=253bp
MADCETKITGQDESIDEIVLICDNGFKQIESKKNTENEFLKKLSLTGFKN
EKFGYDLDVNSQISSIQNIHLNDANLPKDHPKIRNKEHNGIPFKRTSRSA
ITQFHCNKENNSSTKDSVTYSLNKLKPLVVKKHNPSEVSAGYPKNINNNF
RVPLSVKSNSTATSNQDTKIFPPLSSYVKPKPATMPHSPKLSTEIRAKER
NKYNMQLKERENQLKLKKQKEDETKMKDSSKKLEILRKNLIHKPEPIRKY
HP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR027329TPX2_C
Vocabulary: cellular component
TermDefinition
GO:0005819spindle
GO:0005874microtubule
Vocabulary: biological process
TermDefinition
GO:0032147activation of protein kinase activity
GO:0060236regulation of mitotic spindle organization
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 200..224
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 208..252
IPR027329TPX2, C-terminalPFAMPF06886TPX2coord: 191..247
e-value: 2.9E-9
score: 37.0