SMED30013812

Overview
NameSMED30013812
Smed IDSMED30013812
Length (bp)976
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 SMED30013812 (SMED30013812) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013812 (SMED30013812) 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 SMED30013812 (SMED30013812) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30013812 (SMED30013812) 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



SMED30013812

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
intestinal phagocyteSMED30013812SMESG000053906.1 Contig4677GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30013812SMESG000026093.1 Contig4677GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
nervous systemSMED30013812SMESG000026093.1 dd_Smed_v4_6839_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30013812SMESG000026093.1 dd_Smed_v4_6839_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30013812SMESG000026093.1 dd_Smed_v4_6839_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30013812SMESG000026093.1 dd_Smed_v6_6839_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30013812SMESG000026093.1 OX_Smed_1.0.23388ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30013812 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002686:4734..5740 -4197
Homology
[Close]
BLAST of SMED30013812 vs. TrEMBL
Match: A0A183S7D9 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS137 PE=4 SV=1)

HSP 1 Score: 125.561 bits (314), Expect = 2.469e-30
Identity = 65/152 (42.76%), Postives = 92/152 (60.53%), Query Frame = 3 
Query:  195 HIPMSFQSTPSDNQSMIGMMPTGTMSGA----GYVTIPAPRHPSLNQQMVMRDFSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQHILQFLRTLIQ 638
            H+   +   P+    ++ M     +S A     Y T+P    PS++Q M       PP  Q +D+CP ICSLFA+ CCPIT  CS PAL+ SVC+Y+DYR  DM  +R KSD ARRL+I ACI+GLI+   W+++T+LY + +L  L  +I+
Sbjct:  104 HVTTGYPGGPNSGNHVVSMQNPALISAAINSQAYQTLP----PSMSQ-MQSNSAQTPP--QSYDRCPAICSLFAIFCCPITCWCSFPALVYSVCAYSDYRASDMYEYRNKSDVARRLVIIACIIGLILCICWAILTFLYYEPMLALLGDIIR 248
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BLAST of SMED30013812 vs. TrEMBL
Match: A0A0X3Q0M0 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=TR154398 PE=4 SV=1)

HSP 1 Score: 125.176 bits (313), Expect = 3.087e-30
Identity = 65/152 (42.76%), Postives = 92/152 (60.53%), Query Frame = 3 
Query:  195 HIPMSFQSTPSDNQSMIGMMPTGTMSGA----GYVTIPAPRHPSLNQQMVMRDFSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQHILQFLRTLIQ 638
            H+   +   P+    ++ M     +S A     Y T+P    PS++Q M       PP  Q +D+CP ICSLFA+ CCPIT  CS PAL+ SVC+Y+DYR  DM  +R KSD ARRL+I ACI+GLI+   W+++T+LY + +L  L  +I+
Sbjct:  105 HVTTGYPGGPNSGNHVVSMQNPALISAAINSQAYQTLP----PSMSQ-MQSNSAQTPP--QSYDRCPAICSLFAIFCCPITCWCSFPALVYSVCAYSDYRASDMYEYRSKSDVARRLVIIACIIGLILCICWAILTFLYYEPMLALLGDIIR 249
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BLAST of SMED30013812 vs. TrEMBL
Match: G4VIW4 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 GN=Smp_145460 PE=4 SV=1)

HSP 1 Score: 124.79 bits (312), Expect = 1.465e-29
Identity = 58/124 (46.77%), Postives = 83/124 (66.94%), Query Frame = 3 
Query:  270 SGAGYVTIPAPRHPSLNQQMVMRDFSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQHILQFLRTLIQI 641
            S +G + I    H   N   V R    P   + FDKCPI+CSLFA+LCCPIT  CSLPAL+ S+C+Y+DYR  D+ ++R+KSD AR L+ITACIVGL++   W+++T+ Y + +L     +I++
Sbjct:  190 SASGIIGIDQNNH---NNPDVFR----PLSNETFDKCPIVCSLFAILCCPITIWCSLPALVYSLCAYSDYRASDINQYRRKSDIARHLVITACIVGLLLCITWAILTFFYYELMLSVFNDIIRV 306
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BLAST of SMED30013812 vs. TrEMBL
Match: A0A3Q0KP75 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 124.405 bits (311), Expect = 4.157e-29
Identity = 52/101 (51.49%), Postives = 76/101 (75.25%), Query Frame = 3 
Query:  339 DFSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQHILQFLRTLIQI 641
            D  +P   + FDKCPI+CSLFA+LCCPIT  CSLPAL+ S+C+Y+DYR  D+ ++R+KSD AR L+ITACIVGL++   W+++T+ Y + +L     +I++
Sbjct:  244 DVFRPLSNETFDKCPIVCSLFAILCCPITIWCSLPALVYSLCAYSDYRASDINQYRRKSDIARHLVITACIVGLLLCITWAILTFFYYELMLSVFNDIIRV 344
[Close]
BLAST of SMED30013812 vs. TrEMBL
Match: A0A183R0S3 (Uncharacterized protein OS=Schistosoma rodhaini OX=6188 PE=4 SV=1)

HSP 1 Score: 122.865 bits (307), Expect = 1.445e-28
Identity = 51/101 (50.50%), Postives = 75/101 (74.26%), Query Frame = 3 
Query:  339 DFSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQHILQFLRTLIQI 641
            D  +P   + FDKCPI+CSLFA+LCCPIT  CSLPAL+ S+C+Y+DYR  D+ ++R+KSD AR L+IT+CIVGL++   W+++T+ Y + +L     +I +
Sbjct:  244 DAFRPLSNETFDKCPIVCSLFAILCCPITIWCSLPALVYSLCAYSDYRASDINQYRRKSDIARHLVITSCIVGLLLCITWAILTFFYYELMLSVFNDIIHV 344
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BLAST of SMED30013812 vs. Planmine SMEST
Match: SMESG000026093.1 (SMESG000026093.1)

HSP 1 Score: 350.903 bits (899), Expect = 3.298e-123
Identity = 169/169 (100.00%), Postives = 169/169 (100.00%), Query Frame = 3 
Query:  156 MHNKSDMYDISSTHIPMSFQSTPSDNQSMIGMMPTGTMSGAGYVTIPAPRHPSLNQQMVMRDFSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQHILQFLRTLIQINRDKKNQ 662
            MHNKSDMYDISSTHIPMSFQSTPSDNQSMIGMMPTGTMSGAGYVTIPAPRHPSLNQQMVMRDFSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQHILQFLRTLIQINRDKKNQ
Sbjct:    1 MHNKSDMYDISSTHIPMSFQSTPSDNQSMIGMMPTGTMSGAGYVTIPAPRHPSLNQQMVMRDFSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQHILQFLRTLIQINRDKKNQ 169
[Close]
BLAST of SMED30013812 vs. Planmine SMEST
Match: SMESG000004480.1 (SMESG000004480.1)

HSP 1 Score: 120.939 bits (302), Expect = 7.372e-33
Identity = 64/130 (49.23%), Postives = 83/130 (63.85%), Query Frame = 3 
Query:  252 MPTGTMSGAGYVTIPAPRHPSLNQQMVMRDFSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQHILQFLRTLIQI 641
            MPT   + +    IP PR    N+Q V      P    PFDKCPII SL +L  CPIT CCSLPA + S+CSY D+RV D+ RFR  SD A+RLII ACI+GL++V  WS+  Y+Y+ H+L+ L   I++
Sbjct:   71 MPTMQSAPSQPFLIPMPR----NRQTV------PKSMPPFDKCPIIFSLLSLCLCPITCCCSLPAFVFSLCSYVDHRVRDVDRFRINSDYAKRLIIVACILGLLLVVIWSIFVYIYKDHMLRLLSEHIKL 190
[Close]
BLAST of SMED30013812 vs. Planmine SMEST
Match: SMESG000045809.1 (SMESG000045809.1)

HSP 1 Score: 73.559 bits (179), Expect = 1.134e-15
Identity = 45/146 (30.82%), Postives = 71/146 (48.63%), Query Frame = 3 
Query:  213 QSTPSDNQSMIGMMPTGTMSGAGYVTIPAPRHPSLNQQMVMRD----FSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQHILQFLRTLIQ 638
            Q   S+N S IG +  GT     Y        P+L Q+ + RD    F      Q F +   IC++ + + CP+T CCSL   ++S+ SY D RV D + + KK+ C+ +L   A I+G +++ G  ++       I  FL   I+
Sbjct:    5 QQNSSENHSTIGSLK-GTFRSTDYT-------PTLRQEFINRDGNYIFHDSRKIQSFKRFSTICNVCSCVFCPLTLCCSLYGCVISILSYADNRVGDNRNYAKKNSCSSKLAFLAIIIGFLLLIGICIIMVFCGPGICLFLIDFIK 142
[Close]
BLAST of SMED30013812 vs. Planmine SMEST
Match: SMESG000060923.1 (SMESG000060923.1)

HSP 1 Score: 45.8246 bits (107), Expect = 8.619e-6
Identity = 24/68 (35.29%), Postives = 37/68 (54.41%), Query Frame = 3 
Query:  384 IICSLFALLCCPITYCCSLPALILSVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLM 587
            ++CS+  L  CP T CCS  A + S+  Y D+R  D Q +  K   +R L + A ++G +I  G+  M
Sbjct:  104 LVCSIIYLWFCPWTCCCSSTACLYSMGGYVDWRSGDFQAYEFKMRRSRCLAVVAVVLGTVIGLGFLAM 171
The following BLAST results are available for this feature:
BLAST of SMED30013812 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 SMED30013812 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 SMED30013812 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 SMED30013812 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 SMED30013812 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 SMED30013812 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 SMED30013812 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 SMED30013812 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183S7D92.469e-3042.76Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A0X3Q0M03.087e-3042.76Uncharacterized protein OS=Schistocephalus solidus... [more]
G4VIW41.465e-2946.77Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A3Q0KP754.157e-2951.49Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A183R0S31.445e-2850.50Uncharacterized protein OS=Schistosoma rodhaini OX... [more]
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BLAST of SMED30013812 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 SMED30013812 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 SMED30013812 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 SMED30013812 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 SMED30013812 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 SMED30013812 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000026093.13.298e-123100.00SMESG000026093.1[more]
SMESG000004480.17.372e-3349.23SMESG000004480.1[more]
SMESG000045809.11.134e-1530.82SMESG000045809.1[more]
SMESG000060923.18.619e-635.29SMESG000060923.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013812 ID=SMED30013812|Name=SMED30013812|organism=Schmidtea mediterranea sexual|type=transcript|length=976bp
AAAAAAAAATTCTGTATGTTTTTAAATTCATTTACAGTTGCCAATATTTA
TTAAATTTGATTTAGCCGTTGATTATGGTTATTTCATCAAAAAGTATTTG
GAAAATATTATTGGAAAATTTTATTGGGATTTAGTTTCGAAAAAAAAAGA
AAGAAATGCACAATAAATCGGATATGTATGACATTTCTTCGACTCACATT
CCAATGTCATTTCAAAGCACCCCGTCTGATAATCAAAGTATGATTGGCAT
GATGCCAACAGGAACAATGTCTGGTGCTGGTTATGTAACTATTCCTGCTC
CAAGACATCCAAGTTTAAATCAGCAAATGGTAATGAGGGATTTTTCCCAA
CCTCCAATGGGCCAACCCTTTGATAAGTGCCCTATAATCTGTAGTCTATT
TGCTCTGCTGTGCTGTCCAATCACCTATTGCTGTTCGTTGCCAGCACTCA
TTCTCTCAGTTTGCAGTTATACTGATTATCGAGTACATGATATGCAACGG
TTCCGCAAGAAAAGTGACTGCGCAAGAAGACTGATTATCACAGCCTGTAT
AGTTGGTTTAATTATTGTTACTGGATGGTCCTTAATGACATACCTCTATC
GGCAACATATTTTACAGTTTTTACGTACACTTATCCAAATAAATAGGGAT
AAAAAAAATCAATAGTCACTGTGTAAGAAATATGATTACTCATTTAAACG
TTGATTTTTATTAATTAACATTTATGAAATCTATTTTAAAAAATTTAAGA
AAAAAAAATCTTTTGTCAAGTATTATCTTCTGAAACTGTAAGTAGAAAAT
GAAACCGATTTATTCATTTATTTTTAAGGTTTTCAGTTATATAAAACGCG
AATGATAACGTTTGAGTTTTTTTAATGTTCTTATTTTTGAATATGAATTC
TTATTGTGTGTGTGTTGTTGAAATGGAACCTTTCCAATTGTAATTCGGTC
CAGTAGCCTTGATAAATAATAATTTA
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protein sequence of SMED30013812-orf-1

>SMED30013812-orf-1 ID=SMED30013812-orf-1|Name=SMED30013812-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=170bp
MHNKSDMYDISSTHIPMSFQSTPSDNQSMIGMMPTGTMSGAGYVTIPAPR
HPSLNQQMVMRDFSQPPMGQPFDKCPIICSLFALLCCPITYCCSLPALIL
SVCSYTDYRVHDMQRFRKKSDCARRLIITACIVGLIIVTGWSLMTYLYRQ
HILQFLRTLIQINRDKKNQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR007593CD225/Dispanin_fam
Vocabulary: biological process
TermDefinition
GO:0009607response to biotic stimulus
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR007593CD225/Dispanin familyPFAMPF04505CD225coord: 77..139
e-value: 1.7E-6
score: 28.1
NoneNo IPR availableTMHMMTMhelixcoord: 78..100
NoneNo IPR availableTMHMMTMhelixcoord: 126..148