SMED30034523

Overview
NameSMED30034523
Smed IDSMED30034523
Length (bp)1131
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 SMED30034523 (SMED30034523) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034523 (SMED30034523) 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 SMED30034523 (SMED30034523) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30034523 (SMED30034523) 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



SMED30034523

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30034523h1SMcG0014713 SmedASXL_012931SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30034523h1SMcG0014713 dd_Smed_v4_12682_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30034523h1SMcG0014713 dd_Smed_v4_12682_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30034523h1SMcG0014713 dd_Smed_v6_12682_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
testisSMED30034523h1SMcG0014713 DN311687.1smed_ncbi_20240424PMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
epidermisSMED30034523h1SMcG0014713 dd_Smed_v4_12682_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30034523 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001112:85608..91279 +5541
Homology
[Close]
BLAST of SMED30034523 vs. Planmine SMEST
Match: SMESG000009543.1 (SMESG000009543.1)

HSP 1 Score: 568.155 bits (1463), Expect = 0.000e+0
Identity = 314/315 (99.68%), Postives = 314/315 (99.68%), Query Frame = 3 
Query:   81 MPQAHHRIKSEYAKSFKTFSDSAQSEYSENVKFRLARRNQEVSHQPWAWLDVDLXXXXXXXXXXXXHILNDKKQSNKVNCIEISDSSSTETNSDFDASGAVDRPDNFSQFNEQKLLEDLKKKAIERAMEMKSGQRDPQTNESNNLLRRPRHPVKGNSKTFQRSNSSDGHRNKPNRKPPQDLCSINRDKLFLXXXXXXXXXXXXRKKTFNIKSEIDVYPSAVRASKSRDLTKKQKEKSANNPDSGLPKTAMPGKXXXXXXXXXXXXDVDNRAAMEWLSEYQCRFPIYDNEVYKRGLANLAPRGQFARLDTPRTCRI 1025
            MPQAHHRIKSEYAKSFKTFSDSAQSEYSENVKFRLARRNQEVSHQPWAWLDVDLSENESEENSANNHILNDKKQSNKVNCIEISDSSSTETNSDFDASGAVDRPDNFSQFNEQKLLEDLKKKAIERAMEMKSGQRDPQTNESNNLLRRPRHPVKGNSKTFQRSNSSDGHRNKPNRKPPQDLCSINRDKLFLSYGWGSQSSESSRKKTFNIKSEIDVYPSAVRASKSRDLTKKQKEKSANNPD GLPKTAMPGKSSNIPNSSRRSIDVDNRAAMEWLSEYQCRFPIYDNEVYKRGLANLAPRGQFARLDTPRTCRI
Sbjct:    1 MPQAHHRIKSEYAKSFKTFSDSAQSEYSENVKFRLARRNQEVSHQPWAWLDVDLSENESEENSANNHILNDKKQSNKVNCIEISDSSSTETNSDFDASGAVDRPDNFSQFNEQKLLEDLKKKAIERAMEMKSGQRDPQTNESNNLLRRPRHPVKGNSKTFQRSNSSDGHRNKPNRKPPQDLCSINRDKLFLSYGWGSQSSESSRKKTFNIKSEIDVYPSAVRASKSRDLTKKQKEKSANNPDLGLPKTAMPGKSSNIPNSSRRSIDVDNRAAMEWLSEYQCRFPIYDNEVYKRGLANLAPRGQFARLDTPRTCRI 315
The following BLAST results are available for this feature:
BLAST of SMED30034523 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 SMED30034523 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 SMED30034523 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 SMED30034523 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 SMED30034523 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 SMED30034523 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 SMED30034523 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 SMED30034523 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 SMED30034523 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 SMED30034523 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 SMED30034523 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 SMED30034523 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 SMED30034523 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 SMED30034523 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000009543.10.000e+099.68SMESG000009543.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034523 ID=SMED30034523|Name=SMED30034523|organism=Schmidtea mediterranea sexual|type=transcript|length=1131bp
ATTAAATTCGTTGTTAAGATAATTATTAAATAATATTTTTAGAAAATTTT
AATACTAAACAATCAACAAATTTTACAAAAATGCCACAAGCACATCATCG
AATAAAATCTGAATATGCAAAATCTTTTAAAACATTTTCAGATTCTGCAC
AATCAGAATATTCGGAAAATGTAAAATTTCGACTGGCACGTCGCAATCAG
GAAGTATCACATCAGCCATGGGCGTGGTTGGATGTTGATTTAAGTGAAAA
TGAAAGCGAAGAAAATTCCGCTAATAATCATATCCTTAATGATAAAAAAC
AGTCTAACAAAGTTAATTGTATTGAAATTTCTGATTCCAGTTCCACTGAA
ACCAACTCAGATTTTGATGCATCTGGTGCTGTTGATAGACCAGATAATTT
TTCTCAATTTAATGAACAAAAACTACTTGAGGACCTAAAAAAGAAAGCCA
TTGAAAGGGCGATGGAAATGAAATCGGGGCAGCGAGACCCTCAGACTAAT
GAATCGAACAATCTTCTTAGACGTCCTCGTCATCCTGTGAAAGGTAACTC
TAAAACATTCCAACGCAGTAATAGCTCAGATGGGCATCGAAACAAACCTA
ATAGGAAACCTCCGCAAGACTTATGTTCGATTAACCGTGATAAATTATTT
CTCTCCTACGGCTGGGGCTCCCAATCATCTGAAAGCAGTCGAAAGAAAAC
CTTTAATATAAAGTCAGAAATTGATGTTTATCCGTCGGCAGTCAGAGCGT
CGAAATCTCGAGATTTGACTAAGAAACAAAAAGAAAAATCGGCAAATAAC
CCAGATTCGGGACTACCGAAAACTGCGATGCCTGGGAAATCAAGCAATAT
TCCCAATTCTAGTCGGCGCAGCATTGATGTGGATAACCGCGCGGCAATGG
AATGGCTATCGGAGTACCAATGTAGATTCCCAATATACGATAACGAGGTG
TACAAGCGCGGATTGGCTAACCTTGCTCCTCGTGGTCAATTCGCCCGATT
AGATACACCTCGTACTTGCAGGATTTGATTCCACACTGGCCTTTTATTTT
GTCGTTCAAAGTTATTCAATATTTCTTCAATAAGAGCAAATATATTTCCC
CTTGATTGTTTTTGATTTGTCTTTTCTGTGC
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protein sequence of SMED30034523-orf-1

>SMED30034523-orf-1 ID=SMED30034523-orf-1|Name=SMED30034523-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=316bp
MPQAHHRIKSEYAKSFKTFSDSAQSEYSENVKFRLARRNQEVSHQPWAWL
DVDLSENESEENSANNHILNDKKQSNKVNCIEISDSSSTETNSDFDASGA
VDRPDNFSQFNEQKLLEDLKKKAIERAMEMKSGQRDPQTNESNNLLRRPR
HPVKGNSKTFQRSNSSDGHRNKPNRKPPQDLCSINRDKLFLSYGWGSQSS
ESSRKKTFNIKSEIDVYPSAVRASKSRDLTKKQKEKSANNPDSGLPKTAM
PGKSSNIPNSSRRSIDVDNRAAMEWLSEYQCRFPIYDNEVYKRGLANLAP
RGQFARLDTPRTCRI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000208testis
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR029774CSAP
Vocabulary: cellular component
TermDefinition
GO:0005856cytoskeleton
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR029774Centriole, cilia and spindle-associated proteinPFAMPF15748CCSAPcoord: 8..281
e-value: 5.9E-21
score: 75.8
IPR029774Centriole, cilia and spindle-associated proteinPANTHERPTHR31022UNCHARACTERIZEDcoord: 6..280
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 128..183
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 85..108
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 222..262