SMED30006734

Overview
NameSMED30006734
Smed IDSMED30006734
Length (bp)659
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 SMED30006734 (SMED30006734) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30006734 (SMED30006734) 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 SMED30006734 (SMED30006734) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30006734 (SMED30006734) 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



SMED30006734

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
non-ciliated neuronSMED30006734SMESG000010564.1 dd_Smed_v4_8271_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30006734SMESG000010564.1 dd_Smed_v4_8271_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
Homology
[Close]
BLAST of SMED30006734 vs. TrEMBL
Match: A0A226D4I7 (Putative AC transposase OS=Folsomia candida OX=158441 GN=Fcan01_25450 PE=4 SV=1)

HSP 1 Score: 102.834 bits (255), Expect = 6.044e-31
Identity = 53/114 (46.49%), Postives = 77/114 (67.54%), Query Frame = -1 
Query:  267 EWTFQRNHRYINVILHSESK-FWNVGLLRINGSLLAVKWVFV*YDKWNQYGLTSGKNILSLTNDDAAVLQKVGKLVPTAQQLCFLHTIQLAVVDVLYKK-NTTKYRNRSPNESI 602
            EW+  +N RY+NVILH + + FWN+GL+RI+GSL A K + +  +K     L+   +I+ +  D ++V+ K+G+L PT QQLCF H IQL V+DVLYKK N T   + S NE++
Sbjct:  191 EWSSIKNRRYMNVILHGKPQEFWNLGLIRIHGSLPAEKCLEMVANKLRLLNLSLENDIVCIITDGSSVMTKIGRLSPTYQQLCFAHGIQLGVLDVLYKKINQTPEADESENENL 304

HSP 2 Score: 60.077 bits (144), Expect = 6.044e-31
Identity = 31/50 (62.00%), Postives = 35/50 (70.00%), Query Frame = -3 
Query:    1 ITHNQLGPFIQKVR*IVKIFTRSPTKNETLQNYVNLEFGKEFCLILDSKT 150
            I+H  L P I KVR IV++F RSP KNE LQ Y+  EFGKE  LILD KT
Sbjct:  335 ISHT-LRPVIDKVRTIVRMFRRSPLKNEILQTYIKQEFGKELSLILDCKT 383
[Close]
BLAST of SMED30006734 vs. TrEMBL
Match: A0A4C2AGX5 (Uncharacterized protein OS=Eumeta variegata OX=151549 GN=EVAR_71113_1 PE=4 SV=1)

HSP 1 Score: 86.2705 bits (212), Expect = 1.588e-22
Identity = 41/102 (40.20%), Postives = 67/102 (65.69%), Query Frame = -1 
Query:  309 EWTFQRNHRYINVILHS----ESKFWNVGLLRINGSLLAVKWVFV*YDKWNQYGLTSGKNILSLTNDDAAVLQKVGKLVPTAQQLCFLHTIQLAVVDVLYKK 602
            EWT   N R++NV +H+    +  +WN+GL RI GS+ +   V V  +K +++ L+  K+I+ +T D A+V++KVG+L+    QLC+ H +QL + DV+YKK
Sbjct:   73 EWTSGINQRFLNVNVHTVINCQPTYWNIGLARIFGSMSSESCVQVLKEKLSEFDLSLDKDIVGITTDGASVMKKVGRLIEPLLQLCYAHGVQLGITDVIYKK 174

HSP 2 Score: 48.1358 bits (113), Expect = 1.588e-22
Identity = 31/67 (46.27%), Postives = 38/67 (56.72%), Query Frame = -3 
Query:    1 NEDGLVMDYEIQRRCTEITHNQLGPFIQKVR*IVKIFTRSPTKNETLQNYVNLEFGKEFCLILDSKT 201
            N DGL     I R+    T  Q+   I K+R  VK+F  SPTKN+ LQ Y+  EFGK   L+LD KT
Sbjct:  207 NYDGLYFSLPI-RQVYLATEYQM--IISKLRKCVKLFKNSPTKNDMLQIYIQQEFGKTIQLVLDCKT 270
[Close]
BLAST of SMED30006734 vs. TrEMBL
Match: A0A4Y2THF1 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_265140_1 PE=4 SV=1)

HSP 1 Score: 98.5969 bits (244), Expect = 4.293e-22
Identity = 48/103 (46.60%), Postives = 69/103 (66.99%), Query Frame = -1 
Query:  297 EWTFQRNHRYINVILHSESKFWNVGLLRINGSLLAVKWVFV*YDK-WNQYGLTSGKNILSLTNDDAAVLQKVGKLVPTAQQLCFLHTIQLAVVDVLYKKNTTK 602
            EWT Q+NHRY+N+ +H + K +N+GL+RI+GS  A   + +   K    +G  S  +I+ +T D A+V+ K GKL+   QQLCF H +QLAVVD+LYKKN  +
Sbjct:   78 EWTSQKNHRYLNLNVHHKEKRFNLGLIRIHGSCTAEHTISLTKQKRLESFGFDSDTDIIGVTTDGASVMVKFGKLMSCYQQLCFAHGLQLAVVDILYKKNIER 180
[Close]
BLAST of SMED30006734 vs. TrEMBL
Match: A0A4Y2QRS0 (BED-type domain-containing protein OS=Araneus ventricosus OX=182803 GN=AVEN_88722_1 PE=4 SV=1)

HSP 1 Score: 101.293 bits (251), Expect = 4.455e-22
Identity = 48/105 (45.71%), Postives = 70/105 (66.67%), Query Frame = -1 
Query:  288 EWTFQRNHRYINVILHSESKFWNVGLLRINGSLLAVKWVFV*YDKWNQYGLTSGKNILSLTNDDAAVLQKVGKLVPTAQQLCFLHTIQLAVVDVLYKKNTTKYRN 602
            EWT Q+NHRY+N+ +H + K +N+ L+RI+GS  A   + +   +   +GL S  +I+ +T D A+V+ KV KL+    QLCF H +QLA+VD+LYKKN  K RN
Sbjct:  194 EWTSQKNHRYLNLNVHHKEKHFNLSLIRIHGSCTAEHTISLIKTRLESFGLDSDTDIIVVTTDGASVMIKVCKLMSCYHQLCFAHGLQLAMVDILYKKNIEKKRN 298
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BLAST of SMED30006734 vs. TrEMBL
Match: A0A4C1SVE1 (AC transposase OS=Eumeta variegata OX=151549 GN=EVAR_3373_1 PE=4 SV=1)

HSP 1 Score: 82.8037 bits (203), Expect = 5.853e-22
Identity = 43/108 (39.81%), Postives = 65/108 (60.19%), Query Frame = -1 
Query:  279 EWTFQRNHRYINVILHSESKFWNVGLLRINGSLLAVKWVFV*YDKWNQYGLTSGKNILSLTNDDAAVLQKVGKLVPTAQQLCFLHTIQLAVVDVLYKKNTTKYRNRSP 602
            EWT   N RY+ + +HS  KFWN+GL+ I G++ A   + +  ++ +++ ++   +I ++  D   V+ KVG+LV   QQLC  H I LAV DVLYKK+   Y   SP
Sbjct:  175 EWTSMSNKRYMALNVHSYKKFWNLGLVPIYGNMTAENCLRILNERLSKFDISLETDIAAIVTDGPNVMIKVGRLVCAEQQLCLAHGINLAVCDVLYKKHN--YLQDSP 280

HSP 2 Score: 49.6766 bits (117), Expect = 5.853e-22
Identity = 31/72 (43.06%), Postives = 44/72 (61.11%), Query Frame = -3 
Query:    1 NEDGLVMDYE---IQRRCTEITHNQ-LGPFIQKVR*IVKIFTRSPTKNET-LQNYVNLEFGKEFCLILDSKT 201
            +E GL++  +    +    E+T ++ +   I+KVR +V  F RSP KNET LQ YV +E GKE  L+LD KT
Sbjct:  300 SESGLILMSQNDLAREHIPELTQDENIKELIEKVRKVVIYFKRSPLKNETVLQKYVKIEHGKELSLLLDCKT 371
[Close]
BLAST of SMED30006734 vs. Planmine SMEST
Match: SMESG000036917.1 (SMESG000036917.1)

HSP 1 Score: 91.2781 bits (225), Expect = 4.205e-21
Identity = 47/114 (41.23%), Postives = 71/114 (62.28%), Query Frame = -1 
Query:  285 GEWTFQRNHRYINVILH-------SESKFWNVGLLRINGSLLAVKWVFV*YDKWNQYGLTSGKNILSLTNDDAAVLQKVGKLVPTAQQLCFLHTIQLAVVDVLYKKNTTKYRNR 605
             +WT +RN RYIN+ +H       +E+KF ++G++RI+GS+ + K   +   K   + +   KNI+ +T D A+V+ KVG LV   Q LCF H IQL V+D+LY K+  KY N+
Sbjct:  235 NDWTSKRNRRYININIHYAVEHKITEAKFCSLGMVRIHGSMHSEKCKLIVKTKLQDFNINLEKNIVCMTADGASVILKVGSLVSNYQLLCFAHGIQLVVIDILYTKD--KYSNQ 346
[Close]
BLAST of SMED30006734 vs. Planmine SMEST
Match: SMESG000036917.1 (SMESG000036917.1)

HSP 1 Score: 91.2781 bits (225), Expect = 4.705e-21
Identity = 47/114 (41.23%), Postives = 71/114 (62.28%), Query Frame = -1 
Query:  285 GEWTFQRNHRYINVILH-------SESKFWNVGLLRINGSLLAVKWVFV*YDKWNQYGLTSGKNILSLTNDDAAVLQKVGKLVPTAQQLCFLHTIQLAVVDVLYKKNTTKYRNR 605
             +WT +RN RYIN+ +H       +E+KF ++G++RI+GS+ + K   +   K   + +   KNI+ +T D A+V+ KVG LV   Q LCF H IQL V+D+LY K+  KY N+
Sbjct:  235 NDWTSKRNRRYININIHYAVEHKITEAKFCSLGMVRIHGSMHSEKCKLIVKTKLQDFNINLEKNIVCMTADGASVILKVGSLVSNYQLLCFAHGIQLVVIDILYTKD--KYSNQ 346
[Close]
BLAST of SMED30006734 vs. Planmine SMEST
Match: SMESG000036917.1 (SMESG000036917.1)

HSP 1 Score: 91.2781 bits (225), Expect = 5.109e-21
Identity = 47/114 (41.23%), Postives = 71/114 (62.28%), Query Frame = -1 
Query:  285 GEWTFQRNHRYINVILH-------SESKFWNVGLLRINGSLLAVKWVFV*YDKWNQYGLTSGKNILSLTNDDAAVLQKVGKLVPTAQQLCFLHTIQLAVVDVLYKKNTTKYRNR 605
             +WT +RN RYIN+ +H       +E+KF ++G++RI+GS+ + K   +   K   + +   KNI+ +T D A+V+ KVG LV   Q LCF H IQL V+D+LY K+  KY N+
Sbjct:  235 NDWTSKRNRRYININIHYAVEHKITEAKFCSLGMVRIHGSMHSEKCKLIVKTKLQDFNINLEKNIVCMTADGASVILKVGSLVSNYQLLCFAHGIQLVVIDILYTKD--KYSNQ 346
[Close]
BLAST of SMED30006734 vs. Planmine SMEST
Match: SMESG000065760.1 (SMESG000065760.1)

HSP 1 Score: 69.707 bits (169), Expect = 9.444e-14
Identity = 39/99 (39.39%), Postives = 54/99 (54.55%), Query Frame = -1 
Query:  306 EWTFQRNHRYINVILHSESKFWNVGLLRINGSLLAVKWVFV*YDKWNQYGLTSGKNILSLTNDDAAVLQKVGKLVPTAQQLCFLHTIQLAVVDVLYKKN 602
            EWT     RY+NV LHS+   + +GL+ I GS  A +   +   K   YG+   +NIL+ T D A+V++K  +L     Q C  H I LAVV+  Y KN
Sbjct:  154 EWTSCSGKRYLNVTLHSQEDSYKLGLIAIEGSCDAYQIHSLVEQKLMDYGI-KLRNILASTQDGASVMKKYAQLNKIENQFCINHAIHLAVVETFYNKN 251
[Close]
BLAST of SMED30006734 vs. Planmine SMEST
Match: SMESG000018816.1 (SMESG000018816.1)

HSP 1 Score: 66.2402 bits (160), Expect = 2.649e-13
Identity = 40/103 (38.83%), Postives = 58/103 (56.31%), Query Frame = -1 
Query:  297 EWTFQRNHRYINVILHSES-KFWNVGLLRINGSLLAVKWVFV*YDKWNQYGLTSGKNILSLTNDDAAVLQKVGKLVPTAQQLCFLHTIQLAVVDVLYKKNTTK 602
            EWT  +  RY N+ LH  S KF N+GL RINGS  + K+  V  +   Q+G++    I++ T + AAV  K G    T  QLC  H+  LAV+D++  K  ++
Sbjct:    3 EWTSTKMRRYFNINLHDASGKFNNLGLARINGSFNSEKFQQVVRNHLLQFGISFDIYIVACTTNGAAVNIKFGGERTTEFQLCLAHSAYLAVIDIICDKEDSE 105
The following BLAST results are available for this feature:
BLAST of SMED30006734 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 SMED30006734 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 SMED30006734 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 SMED30006734 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 SMED30006734 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 SMED30006734 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 SMED30006734 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 SMED30006734 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A226D4I76.044e-3146.49Putative AC transposase OS=Folsomia candida OX=158... [more]
A0A4C2AGX51.588e-2240.20Uncharacterized protein OS=Eumeta variegata OX=151... [more]
A0A4Y2THF14.293e-2246.60Uncharacterized protein OS=Araneus ventricosus OX=... [more]
A0A4Y2QRS04.455e-2245.71BED-type domain-containing protein OS=Araneus vent... [more]
A0A4C1SVE15.853e-2239.81AC transposase OS=Eumeta variegata OX=151549 GN=EV... [more]
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BLAST of SMED30006734 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 SMED30006734 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 SMED30006734 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 SMED30006734 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 SMED30006734 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 SMED30006734 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000036917.14.205e-2141.23SMESG000036917.1[more]
SMESG000036917.14.705e-2141.23SMESG000036917.1[more]
SMESG000036917.15.109e-2141.23SMESG000036917.1[more]
SMESG000065760.19.444e-1439.39SMESG000065760.1[more]
SMESG000018816.12.649e-1338.83SMESG000018816.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006734 ID=SMED30006734|Name=SMED30006734|organism=Schmidtea mediterranea sexual|type=transcript|length=659bp
AGTCTTGGAATCTAAGATTAAGCAAAATTCTTTGCCAAATTCGAGATTTA
CATAATTTTGTAGTGTTTCATTTTTTGTCGGTGAACGTGTAAATATTTTC
ACAATTTATCTGACTTTTTGTATAAACGGACCAAGCTGATTATGGGTTAT
TTCTGTACATCGTCGCTGTATTTCGTAATCCATTACTAATCCATCCTCAT
TTGCATATCTCCTTTGACTGCATCATAAAATTTGGATTCTTCGGTTTCGG
AATCTCAATCAATGTAAATTGACTCATTTGGACTTCTGTTTCTATATTTA
GTTGTATTTTTTTTATAAAGAACATCTACGACCGCAAGTTGTATCGTATG
GAGAAAACACAATTGCTGGGCAGTCGGTACTAATTTGCCTACTTTCTGCA
AAACTGCAGCATCATCATTTGTTAAAGACAGAATATTTTTACCCGATGTC
AAACCATACTGATTCCATTTGTCATATTAAACAAAAACCCATTTTACTGC
AAGTAAACTTCCATTGATTCGGAGAAGTCCTACGTTCCAAAATTTTGATT
CGGAATGAAGAATCACATTTATGTATCGATGATTCCTTTGAAAGGTCCAC
TCACCGAAATTAATACTATAAATATAAATGAAAAATTTGATAAAAAAAGT
AAAGACTGG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell