SMED30004939

Overview
NameSMED30004939
Smed IDSMED30004939
Length (bp)863
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 SMED30004939 (SMED30004939) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004939 (SMED30004939) 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 SMED30004939 (SMED30004939) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004939 (SMED30004939) 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



SMED30004939

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30004939SMESG000064545.1 SMESG000047762.1 SMESG000046800.1 SMESG000012864.1 SMESG000003895.1 SMESG000070132.1 SMESG000068326.1 SMESG000067883.1 SMESG000062229.1 SMESG000061668.1 SMESG000058705.1 SMESG000030728.1 SMESG000022905.1 SMESG000020613.1 Contig65GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004939SMESG000076325.1 Contig4281GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004939SMESG000001797.1 Contig4281GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004939SMESG000001797.1 Contig65GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gamma neoblastSMED30004939SMESG000001797.1 SMED30004939smed_20140614PMID:29906446
Zeng et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30004939SMESG000001797.1 dd_Smed_v4_272_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30004939SMESG000001797.1 dd_Smed_v4_272_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30004939SMESG000001797.1 dd_Smed_v4_272_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30004939SMESG000001797.1 dd_Smed_v4_272_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30004939SMESG000001797.1 dd_Smed_v4_272_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004939SMESG000001797.1 SMESG000005752.1 Contig23542newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004939SMESG000001797.1 SMESG000005752.1 Contig23542uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
intestinal phagocyteSMED30004939SMESG000001797.1 dd_Smed_v6_272_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30004939 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006425:1707..2569 +4288
Homology
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BLAST of SMED30004939 vs. Planmine SMEST
Match: SMESG000001797.1 (SMESG000001797.1)

HSP 1 Score: 207.223 bits (526), Expect = 1.877e-67
Identity = 105/107 (98.13%), Postives = 106/107 (99.07%), Query Frame = 2 
Query:  161 MNQASEFCTGLKLCDDYCCGSQTGYQYCCSICTASINYNPNSNDCFVINIGAIIGGILSFIAFIVIVSLLVACCCGCICSTRTGIQRRGRVINPPASTVTVISQNQT 481
            MNQASEFCTGLKLCDDYCCGS+TGYQYCCSICTASINYN NSNDCFVINIGAIIGGILSFIAFIVIVSLLVACCCGCICSTRTGIQRRGRVINPPASTVTVISQNQT
Sbjct:    1 MNQASEFCTGLKLCDDYCCGSRTGYQYCCSICTASINYNLNSNDCFVINIGAIIGGILSFIAFIVIVSLLVACCCGCICSTRTGIQRRGRVINPPASTVTVISQNQT 107
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BLAST of SMED30004939 vs. Planmine SMEST
Match: SMESG000001797.1 (SMESG000001797.1)

HSP 1 Score: 189.504 bits (480), Expect = 2.402e-60
Identity = 121/123 (98.37%), Postives = 122/123 (99.19%), Query Frame = 2 
Query:  113 MGKIXXXXXXXXXXXXMNQASEFCTGLKLCDDYCCGSQTGYQYCCSICTASINYNPNSNDCFVINIGAIIGGILSFIAFIVIVSLLVACCCGCICSTRTGIQRRGRVINPPASTVTVISQNQT 481
            MGKIVLQLFTLFTLLVMNQASEFCTGLKLCDDYCCGS+TGYQYCCSICTASINYN NSNDCFVINIGAIIGGILSFIAFIVIVSLLVACCCGCICSTRTGIQRRGRVINPPASTVTVISQNQT
Sbjct:    1 MGKIVLQLFTLFTLLVMNQASEFCTGLKLCDDYCCGSRTGYQYCCSICTASINYNLNSNDCFVINIGAIIGGILSFIAFIVIVSLLVACCCGCICSTRTGIQRRGRVINPPASTVTVISQNQT 123
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BLAST of SMED30004939 vs. Planmine SMEST
Match: SMESG000001790.1 (SMESG000001790.1)

HSP 1 Score: 109.768 bits (273), Expect = 2.630e-29
Identity = 60/108 (55.56%), Postives = 79/108 (73.15%), Query Frame = 2 
Query:  167 QASEFCTGL--KLCDDYCCGSQTG-YQYCCSICTASINYNPNSNDCFVINIGAIIGGILSFIAFIVIVSLLVACCCGCICSTRTGIQRRGRVINPPASTVTVISQNQT 481
            QA EFC+G+    C  YCC   TG  + CC+ C+ SI  +P   +C   ++G+I+GGI+ FIAF++IVSL+VACCCGCICS+RTGIQRRG V++P  +TVTVI  NQT
Sbjct:   15 QAGEFCSGILSPYCPSYCCRYNTGGIESCCTTCSFSIRNHP---EC---DVGSIVGGIIGFIAFVIIVSLIVACCCGCICSSRTGIQRRGWVVSPATTTVTVIDSNQT 116
[Close]
BLAST of SMED30004939 vs. Planmine SMEST
Match: SMESG000001789.1 (SMESG000001789.1)

HSP 1 Score: 102.064 bits (253), Expect = 3.050e-26
Identity = 55/107 (51.40%), Postives = 71/107 (66.36%), Query Frame = 2 
Query:  167 QASEFC--TGLKLCDDYCCGSQTGYQYCCSICTASINYNPNSNDCFVINIGAIIGGILSFIAFIVIVSLLVACCCGCICSTRTGIQRRGRVINPPASTVTVISQNQT 481
            QA EFC  T    C DYCCG   G   CCS C+ SI  +P   +C     G+I+GGI+ FI F++I+SL+V CCCGCICS RTGI++RG V++P  + VTVI+ N T
Sbjct:   15 QAGEFCSSTASYYCPDYCCGYYNGVPKCCSTCSFSIKSHP---EC---GFGSIVGGIIGFILFVIIISLIVTCCCGCICSNRTGIRKRGWVVSPATNLVTVINPNST 115
[Close]
BLAST of SMED30004939 vs. Planmine SMEST
Match: SMESG000001793.1 (SMESG000001793.1)

HSP 1 Score: 97.4413 bits (241), Expect = 9.688e-25
Identity = 54/106 (50.94%), Postives = 74/106 (69.81%), Query Frame = 2 
Query:  173 SEFCTGLKL-CDDYCCGSQTGYQYCCSICTASINYNPNSNDCFV--INIGAIIGGILSFIAFIVIVSLLVACCCGCICSTRTGIQRRGRVINPPASTVTVISQNQT 481
            +E+C GL + CD YCCG+    + CC  C  S+N++P   +C+   I +G IIGGI SFI F++IVSL++A CCG ICS+RTGIQRRG++I    +TVTV + N T
Sbjct:    2 TEYCKGLSITCDYYCCGTFDNMR-CCKSCVQSLNFHP---ECYTTSITVGPIIGGIASFIIFVIIVSLIIALCCGYICSSRTGIQRRGQIIQTGEATVTVTNPNGT 103
The following BLAST results are available for this feature:
BLAST of SMED30004939 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 SMED30004939 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 SMED30004939 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 SMED30004939 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 SMED30004939 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 SMED30004939 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 SMED30004939 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 SMED30004939 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 SMED30004939 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 SMED30004939 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 SMED30004939 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 SMED30004939 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 SMED30004939 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 SMED30004939 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000001797.11.877e-6798.13SMESG000001797.1[more]
SMESG000001797.12.402e-6098.37SMESG000001797.1[more]
SMESG000001790.12.630e-2955.56SMESG000001790.1[more]
SMESG000001789.13.050e-2651.40SMESG000001789.1[more]
SMESG000001793.19.688e-2550.94SMESG000001793.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004939 ID=SMED30004939|Name=SMED30004939|organism=Schmidtea mediterranea sexual|type=transcript|length=863bp
AGTCTATTCCGTTGCAATGAGAACCTAATGTAGATGGCTTGTGACTTATT
TCAAAATTCTGAATTACTAACACAAATTCTGATTGTTCAGTCATTTTTAT
AGAATTTTCATCATGGGCAAAATTGTTCTTCAACTTTTTACACTATTCAC
TCTACTCGTTATGAATCAGGCCTCCGAGTTTTGCACTGGATTGAAGCTTT
GCGATGATTATTGTTGCGGCAGCCAGACAGGATATCAATATTGCTGCAGC
ATTTGCACAGCTAGCATCAATTACAATCCGAATAGTAATGATTGTTTCGT
TATCAATATCGGAGCTATAATTGGAGGAATTTTAAGCTTCATTGCTTTTA
TCGTCATAGTTTCACTACTTGTAGCTTGTTGTTGCGGCTGTATTTGCTCA
ACTAGAACAGGAATACAAAGGCGAGGCAGAGTAATCAACCCACCAGCATC
GACTGTCACTGTGATAAGTCAAAATCAGACTGCATATCCACCAGGCCAAT
ACACATATCCTCAAGGTCAGCCAGTTTATCCTCAGGGTCAACCAGCTTAT
TATCAAGGTCAACCACCTTATCCTCAAGGTCAACCAGCTTATCTTCAAGG
TCAACCGGCTTATCCACCGACCAATCAAAACTATCAAAATCCTCCACCTT
ACGTTCCTGGATACGCACCGGAAAAACAATAACAAATGTCCTTTGTTAAT
TACTCTACAAACTGAAACTTTATTTTACCTTAATTTAGATTGTTAATAGA
AAAAAGGTTATTAAATCAAATTTGAGAAAATTTATAGTATAAATGTATAA
TTTTTGGGTAGAATTCAGATAAAATAATACTCCCTCCGTTCCAAATATAA
TGTCCGATTTTGC
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protein sequence of SMED30004939-orf-1

>SMED30004939-orf-1 ID=SMED30004939-orf-1|Name=SMED30004939-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=190bp
MGKIVLQLFTLFTLLVMNQASEFCTGLKLCDDYCCGSQTGYQYCCSICTA
SINYNPNSNDCFVINIGAIIGGILSFIAFIVIVSLLVACCCGCICSTRTG
IQRRGRVINPPASTVTVISQNQTAYPPGQYTYPQGQPVYPQGQPAYYQGQ
PPYPQGQPAYLQGQPAYPPTNQNYQNPPPYVPGYAPEKQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000039gamma neoblast
PLANA:0000070intestinal phagocyte
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR026910Shisa
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR026910Shisa familyPFAMPF13908Shisacoord: 70..165
e-value: 2.8E-7
score: 31.0
IPR026910Shisa familyPANTHERPTHR31395FAMILY NOT NAMEDcoord: 30..174
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 150..182
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 154..182
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..20
score: 0.861
NoneNo IPR availableTMHMMTMhelixcoord: 66..88