SMED30007506

Overview
NameSMED30007506
Smed IDSMED30007506
Length (bp)452
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 SMED30007506 (SMED30007506) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007506 (SMED30007506) 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 SMED30007506 (SMED30007506) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007506 (SMED30007506) 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



SMED30007506

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
neuronSMED30007506SMESG000071441.1 SMESG000059599.1 SMESG000058180.1 SMESG000047025.1 SMESG000041246.1 SMESG000037745.1 SMESG000013749.1 Contig36213newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30007506SMESG000071441.1 SMESG000059599.1 SMESG000058180.1 SMESG000047025.1 SMESG000041246.1 SMESG000037745.1 SMESG000013749.1 Contig36213uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
reproductive organSMED30007506SMESG000079542.1 SMESG000071441.1 SMESG000059599.1 SMESG000047025.1 SMESG000047024.1 SMESG000046893.1 SMESG000041246.1 SMESG000029087.1 SMESG000013749.1 SMESG000010825.1 SMESG000008086.1 SMESG000077611.1 SMESG000073729.1 SMESG000055578.1 SMESG000055415.1 SMESG000052110.1 SMESG000050492.1 SMESG000039167.1 SMESG000036922.1 SMESG000033763.1 SMESG000027381.1 SMESG000070487.1 SMESG000018675.1 SMESG000018320.1 SMESG000011196.1 SMESG000008519.1 Contig44875newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30007506SMESG000079542.1 SMESG000071441.1 SMESG000059599.1 SMESG000047025.1 SMESG000047024.1 SMESG000046893.1 SMESG000041246.1 SMESG000029087.1 SMESG000013749.1 SMESG000010825.1 SMESG000008086.1 SMESG000077611.1 SMESG000073729.1 SMESG000055578.1 SMESG000055415.1 SMESG000052110.1 SMESG000050492.1 SMESG000039167.1 SMESG000036922.1 SMESG000033763.1 SMESG000027381.1 SMESG000070487.1 SMESG000018675.1 SMESG000018320.1 SMESG000011196.1 SMESG000008519.1 Contig44875uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30007506 vs. TrEMBL
Match: Q76IM9 (Reverse transcriptase OS=Ciona intestinalis OX=7719 GN=rt PE=4 SV=1)

HSP 1 Score: 39.2762 bits (90), Expect = 5.626e-6
Identity = 15/31 (48.39%), Postives = 21/31 (67.74%), Query Frame = 3 
Query:  102 LCRRCHNQDETLPHVLQNCKVHLTLAFNRHN 194
            LCRRC    E+LPHVL +C  ++++   RHN
Sbjct: 1381 LCRRCGASVESLPHVLNHCPPNMSIILGRHN 1411

HSP 2 Score: 38.5058 bits (88), Expect = 5.626e-6
Identity = 26/89 (29.21%), Postives = 44/89 (49.44%), Query Frame = 1 
Query:  178 LLIVTTMPSTNSTSFEKSPSLIAVVNHTCSLVSNTKE--RVDLIITNNKKNTILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAA 438
            L++   + + + T F++    I+V       +S T E  R D++   N   ++++VD+ CPFD    F+   K  L KYD L   I A+
Sbjct: 1412 LVLQEVLNAVDKTQFKE----ISVDRTVPEHMSETGEALRPDIVARRND-GSVVVVDVACPFDQKANFDEAAKRKLLKYDKLCCNIAAS 1495
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BLAST of SMED30007506 vs. Planmine SMEST
Match: SMESG000044382.1 (SMESG000044382.1)

HSP 1 Score: 168.318 bits (425), Expect = 4.584e-53
Identity = 96/158 (60.76%), Postives = 112/158 (70.89%), Query Frame = 1 
Query:    1 FKVELREDPWKFIHRAPTNTFANFAKPYIKVRIDCVGVAITKM-KRCHMFCKIARFILLLLLIVTTMP-STNSTSFEK------SPSLIAVVNHTCSLVSNTKERVDLIITNNKKNTILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAAKPSF 450
            F  ELRED WKFIHRA TNT A FAKPYIK           ++ +RCH   +    +L    +  T+  + ++  F+K      +PSL+ VV+HTCSLVSN+KERVDLIITNN+K TILM DIKCPFDSLVTFETVNKENLAKYDSLKKQIQ AKPSF
Sbjct:   59 FTGELREDHWKFIHRARTNTLAYFAKPYIK--------GENRLSRRCHKQDETLPHVLQNCKVHLTLALNPHNDCFQKIVHHLKNPSLVVVVDHTCSLVSNSKERVDLIITNNEKKTILMFDIKCPFDSLVTFETVNKENLAKYDSLKKQIQDAKPSF 208
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BLAST of SMED30007506 vs. Planmine SMEST
Match: SMESG000079542.1 (SMESG000079542.1)

HSP 1 Score: 141.354 bits (355), Expect = 6.253e-51
Identity = 70/75 (93.33%), Postives = 73/75 (97.33%), Query Frame = 1 
Query:  226 KSPSLIAVVNHTCSLVSNTKERVDLIITNNKKNTILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAAKPSF 450
            KSPSLI VV+HTCSLVSN+KERVDLIITNN+K TILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAAKPSF
Sbjct:  924 KSPSLIVVVDHTCSLVSNSKERVDLIITNNEKKTILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAAKPSF 998

HSP 2 Score: 76.6406 bits (187), Expect = 6.253e-51
Identity = 33/39 (84.62%), Postives = 35/39 (89.74%), Query Frame = 3 
Query:   93 ENRLCRRCHNQDETLPHVLQNCKVHLTLAFNRHNDAFNK 209
            ENRLCRRCHNQD+TLPHVLQNCKVHLTLA NRHND   +
Sbjct:  880 ENRLCRRCHNQDKTLPHVLQNCKVHLTLALNRHNDCLQQ 918
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BLAST of SMED30007506 vs. Planmine SMEST
Match: SMESG000041246.1 (SMESG000041246.1)

HSP 1 Score: 139.813 bits (351), Expect = 9.066e-51
Identity = 69/75 (92.00%), Postives = 73/75 (97.33%), Query Frame = 1 
Query:  226 KSPSLIAVVNHTCSLVSNTKERVDLIITNNKKNTILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAAKPSF 450
            KSPSLI VV+HTCSLVSN+KERVDLIITNN+K TILMVDIKCPFDSLVTF+TVNKENLAKYDSLKKQIQAAKPSF
Sbjct: 1102 KSPSLIVVVDHTCSLVSNSKERVDLIITNNEKKTILMVDIKCPFDSLVTFKTVNKENLAKYDSLKKQIQAAKPSF 1176

HSP 2 Score: 77.7962 bits (190), Expect = 9.066e-51
Identity = 34/41 (82.93%), Postives = 35/41 (85.37%), Query Frame = 3 
Query:   87 KSENRLCRRCHNQDETLPHVLQNCKVHLTLAFNRHNDAFNK 209
            K ENRLCRRCHNQDE LPHVLQNCKVHLTLA NRHND   +
Sbjct: 1056 KRENRLCRRCHNQDEALPHVLQNCKVHLTLALNRHNDCLQQ 1096

HSP 3 Score: 76.2554 bits (186), Expect = 1.126e-16
Identity = 56/155 (36.13%), Postives = 85/155 (54.84%), Query Frame = 1 
Query:   10 ELREDPWKFIHRAPTNTFANFAKPYIKVRIDCVGVAITKM-KRCHMFCKIARFILLLLLI--VTTMPSTNS-----TSFEKSPSLIAVVNHTCSLVSNTKERVDLIITNNKKNTILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAAKPSF 450
            +L E  W FIHRA TNT    AKP         G   +++ +RC    +   + L    I  + T+   N      T+  K+P+ I VV+ + SLV N+K+R ++IIT+ ++  I M+DIKCP DS+  FE  +K N+ KY  L+ ++Q AKP +
Sbjct:  597 KLGEFAWNFIHRARTNTININAKPN--------GKGDSRLCRRCEKEDETMSYALQSCKIYQILTLERHNDCLKIITNNLKNPNFIVVVDSSSSLVLNSKQRDNIIITDTERKRIFMIDIKCPMDSVSHFELTDKANIEKYSLLQSELQVAKPDY 743
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BLAST of SMED30007506 vs. Planmine SMEST
Match: SMESG000041246.1 (SMESG000041246.1)

HSP 1 Score: 139.813 bits (351), Expect = 1.221e-50
Identity = 69/75 (92.00%), Postives = 73/75 (97.33%), Query Frame = 1 
Query:  226 KSPSLIAVVNHTCSLVSNTKERVDLIITNNKKNTILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAAKPSF 450
            KSPSLI VV+HTCSLVSN+KERVDLIITNN+K TILMVDIKCPFDSLVTF+TVNKENLAKYDSLKKQIQAAKPSF
Sbjct: 1148 KSPSLIVVVDHTCSLVSNSKERVDLIITNNEKKTILMVDIKCPFDSLVTFKTVNKENLAKYDSLKKQIQAAKPSF 1222

HSP 2 Score: 77.0258 bits (188), Expect = 1.221e-50
Identity = 33/39 (84.62%), Postives = 34/39 (87.18%), Query Frame = 3 
Query:   93 ENRLCRRCHNQDETLPHVLQNCKVHLTLAFNRHNDAFNK 209
            ENRLCRRCHNQDE LPHVLQNCKVHLTLA NRHND   +
Sbjct: 1104 ENRLCRRCHNQDEALPHVLQNCKVHLTLALNRHNDCLQQ 1142

HSP 3 Score: 76.2554 bits (186), Expect = 1.097e-16
Identity = 56/155 (36.13%), Postives = 85/155 (54.84%), Query Frame = 1 
Query:   10 ELREDPWKFIHRAPTNTFANFAKPYIKVRIDCVGVAITKM-KRCHMFCKIARFILLLLLI--VTTMPSTNS-----TSFEKSPSLIAVVNHTCSLVSNTKERVDLIITNNKKNTILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAAKPSF 450
            +L E  W FIHRA TNT    AKP         G   +++ +RC    +   + L    I  + T+   N      T+  K+P+ I VV+ + SLV N+K+R ++IIT+ ++  I M+DIKCP DS+  FE  +K N+ KY  L+ ++Q AKP +
Sbjct:  597 KLGEFAWNFIHRARTNTININAKPN--------GKGDSRLCRRCEKEDETMSYALQSCKIYQILTLERHNDCLKIITNNLKNPNFIVVVDSSSSLVLNSKQRDNIIITDTERKRIFMIDIKCPMDSVSHFELTDKANIEKYSLLQSELQVAKPDY 743
[Close]
BLAST of SMED30007506 vs. Planmine SMEST
Match: SMESG000071441.1 (SMESG000071441.1)

HSP 1 Score: 171.014 bits (432), Expect = 3.725e-50
Identity = 94/150 (62.67%), Postives = 100/150 (66.67%), Query Frame = 1 
Query:    1 FKVELREDPWKFIHRAPTNTFANFAKPYIKVRIDCVGVAITKMKRCHMFCKIARFILLLLLIVTTMPSTNSTSFEKSPSLIAVVNHTCSLVSNTKERVDLIITNNKKNTILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAAKPSF 450
            FK ELRED WKFIH A TNT ANFAK Y+KV               H+                           KSPSLI VV+HTCSLVSN+KERVDLIITNN+K TILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAA+PSF
Sbjct:  604 FKGELREDHWKFIHHARTNTLANFAKSYLKVH--------------HL---------------------------KSPSLIVVVDHTCSLVSNSKERVDLIITNNEKKTILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAARPSF 712
The following BLAST results are available for this feature:
BLAST of SMED30007506 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 SMED30007506 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 SMED30007506 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 SMED30007506 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 SMED30007506 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 SMED30007506 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 SMED30007506 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 SMED30007506 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
Q76IM95.626e-648.39Reverse transcriptase OS=Ciona intestinalis OX=771... [more]
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BLAST of SMED30007506 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 SMED30007506 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 SMED30007506 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 SMED30007506 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 SMED30007506 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 SMED30007506 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000044382.14.584e-5360.76SMESG000044382.1[more]
SMESG000079542.16.253e-5193.33SMESG000079542.1[more]
SMESG000041246.19.066e-5192.00SMESG000041246.1[more]
SMESG000041246.11.221e-5092.00SMESG000041246.1[more]
SMESG000071441.13.725e-5062.67SMESG000071441.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007506 ID=SMED30007506|Name=SMED30007506|organism=Schmidtea mediterranea sexual|type=transcript|length=452bp
TTTAAAGTAGAATTACGAGAGGATCCTTGGAAGTTTATTCATCGTGCCCC
AACAAACACATTTGCTAATTTTGCAAAACCCTATATAAAAGTGAGAATAG
ATTGTGTAGGCGTTGCCATAACCAAGATGAAACGTTGCCACATGTTTTGC
AAAATTGCAAGGTTCATCTTACTCTTGCTTTTAATCGTCACAACGATGCC
TTCAACAAATAGTACATCATTTGAAAAGTCTCCTTCACTGATTGCTGTTG
TGAACCACACTTGCTCCTTGGTATCAAACACTAAAGAACGAGTCGATTTG
ATTATAACTAATAATAAGAAAAATACAATTCTTATGGTTGATATTAAATG
TCCTTTTGATTCTTTGGTCACGTTTGAAACTGTGAATAAAGAAAATTTGG
CAAAATATGATTCTTTAAAAAAACAAATACAGGCTGCCAAACCTAGCTTT
AC
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protein sequence of SMED30007506-orf-1

>SMED30007506-orf-1 ID=SMED30007506-orf-1|Name=SMED30007506-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=150bp
FKVELREDPWKFIHRAPTNTFANFAKPYIKVRIDCVGVAITKMKRCHMFC
KIARFILLLLLIVTTMPSTNSTSFEKSPSLIAVVNHTCSLVSNTKERVDL
IITNNKKNTILMVDIKCPFDSLVTFETVNKENLAKYDSLKKQIQAAKPSF
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0002089reproductive organ