SMED30031429

Overview
NameSMED30031429
Smed IDSMED30031429
Length (bp)1170
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 SMED30031429 (SMED30031429) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031429 (SMED30031429) 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 SMED30031429 (SMED30031429) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031429 (SMED30031429) 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



SMED30031429

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30031429SMESG000038604.1 dd_Smed_v4_1973_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30031429SMESG000038604.1 dd_Smed_v4_1973_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30031429SMESG000038604.1 dd_Smed_v4_1973_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
Smed sexual biotypeSMED30031429SMESG000038604.1 SMESG000021637.1 Contig38041newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031429SMESG000038604.1 SMESG000021637.1 Contig38041uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30031429 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004905:15077..16154 -3789
Homology
[Close]
BLAST of SMED30031429 vs. TrEMBL
Match: A0A183SGK3 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS3351 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 1.214e-10
Identity = 33/66 (50.00%), Postives = 45/66 (68.18%), Query Frame = 2 
Query:  344 SNRLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKWVGY 541
            SNR F + ETQ++V LF DYF SG CPS  E+R R   + L ++RN TS+R KVKR+ ++ +W  Y
Sbjct:  390 SNRFFDDLETQVVVKLFSDYFTSGSCPSLSEVRHRIANSVLQIHRNATSIRAKVKRLQTSGRWTDY 455
[Close]
BLAST of SMED30031429 vs. TrEMBL
Match: A0A0R3SI42 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS4605 PE=4 SV=1)

HSP 1 Score: 68.9366 bits (167), Expect = 4.431e-10
Identity = 28/62 (45.16%), Postives = 44/62 (70.97%), Query Frame = 2 
Query:  347 NRLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKW 532
            NR F + ETQ +V LF+D+F++G CPS +E+R+R   ++L   RN  S+R KVKR+ ++ +W
Sbjct:  106 NRFFNDYETQFVVKLFRDFFVNGSCPSLNEVRRRIAHSQLQGRRNANSVRAKVKRLQASGRW 167
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BLAST of SMED30031429 vs. TrEMBL
Match: A0A1S8WZ65 (Uncharacterized protein (Fragment) OS=Opisthorchis viverrini OX=6198 GN=X801_04411 PE=4 SV=1)

HSP 1 Score: 69.707 bits (169), Expect = 1.055e-9
Identity = 31/64 (48.44%), Postives = 44/64 (68.75%), Query Frame = 2 
Query:  350 RLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKWVGY 541
            RLF + ET+L+V LF+DYF  G CP  +E+R+RT  T LA  R  TS+R K+KR+ ++ +W  Y
Sbjct:  194 RLFDDFETRLVVKLFRDYFTKGSCPVLNEVRQRTANTVLAGRRTATSIRAKIKRLQTSGRWTDY 257
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BLAST of SMED30031429 vs. TrEMBL
Match: A0A564YWJ1 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=WMSIL1_LOCUS10240 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 3.033e-9
Identity = 28/62 (45.16%), Postives = 44/62 (70.97%), Query Frame = 2 
Query:  347 NRLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKW 532
            NR F + ETQ +V LF+D+F++G CPS +E+R+R   ++L   RN  S+R KVKR+ ++ +W
Sbjct:  295 NRFFNDYETQFVVKLFRDFFVNGSCPSLNEVRRRIAHSQLQGRRNANSVRAKVKRLQASGRW 356
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BLAST of SMED30031429 vs. TrEMBL
Match: A0A4V3SHA2 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_000361 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 3.421e-9
Identity = 31/64 (48.44%), Postives = 44/64 (68.75%), Query Frame = 2 
Query:  350 RLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKWVGY 541
            RLF + ET+L+V LF+DYF  G CP  +E+R+RT  T LA  R  TS+R K+KR+ ++ +W  Y
Sbjct:  314 RLFDDFETRLVVKLFRDYFTKGSCPVLNEVRQRTANTVLAGRRTATSIRAKIKRLQTSGRWTDY 377
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BLAST of SMED30031429 vs. Planmine SMEST
Match: SMESG000038604.1 (SMESG000038604.1)

HSP 1 Score: 275.789 bits (704), Expect = 6.090e-93
Identity = 150/150 (100.00%), Postives = 150/150 (100.00%), Query Frame = 2 
Query:  104 MNSDSQNSYPMLPPKLNETERMVHVQHWINNLPIDVEXXXXXXXXXXXXXXXXLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKWVGYIRHS 553
            MNSDSQNSYPMLPPKLNETERMVHVQHWINNLPIDVESCSYAPSAPDSSSDSCLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKWVGYIRHS
Sbjct:    1 MNSDSQNSYPMLPPKLNETERMVHVQHWINNLPIDVESCSYAPSAPDSSSDSCLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKWVGYIRHS 150
[Close]
BLAST of SMED30031429 vs. Planmine SMEST
Match: SMESG000038604.1 (SMESG000038604.1)

HSP 1 Score: 254.603 bits (649), Expect = 8.995e-85
Identity = 140/140 (100.00%), Postives = 140/140 (100.00%), Query Frame = 2 
Query:  134 MLPPKLNETERMVHVQHWINNLPIDVEXXXXXXXXXXXXXXXXLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKWVGYIRHS 553
            MLPPKLNETERMVHVQHWINNLPIDVESCSYAPSAPDSSSDSCLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKWVGYIRHS
Sbjct:    1 MLPPKLNETERMVHVQHWINNLPIDVESCSYAPSAPDSSSDSCLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKWVGYIRHS 140
[Close]
BLAST of SMED30031429 vs. Planmine SMEST
Match: SMESG000038604.1 (SMESG000038604.1)

HSP 1 Score: 144.436 bits (363), Expect = 1.974e-42
Identity = 87/87 (100.00%), Postives = 87/87 (100.00%), Query Frame = 2 
Query:  104 MNSDSQNSYPMLPPKLNETERMVHVQHWINNLPIDVEXXXXXXXXXXXXXXXXLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTE 364
            MNSDSQNSYPMLPPKLNETERMVHVQHWINNLPIDVESCSYAPSAPDSSSDSCLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTE
Sbjct:    1 MNSDSQNSYPMLPPKLNETERMVHVQHWINNLPIDVESCSYAPSAPDSSSDSCLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTE 87
[Close]
BLAST of SMED30031429 vs. Planmine SMEST
Match: SMESG000038604.1 (SMESG000038604.1)

HSP 1 Score: 124.405 bits (311), Expect = 6.932e-35
Identity = 77/77 (100.00%), Postives = 77/77 (100.00%), Query Frame = 2 
Query:  134 MLPPKLNETERMVHVQHWINNLPIDVEXXXXXXXXXXXXXXXXLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTE 364
            MLPPKLNETERMVHVQHWINNLPIDVESCSYAPSAPDSSSDSCLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTE
Sbjct:    1 MLPPKLNETERMVHVQHWINNLPIDVESCSYAPSAPDSSSDSCLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTE 77
[Close]
BLAST of SMED30031429 vs. Planmine SMEST
Match: SMESG000064860.1 (SMESG000064860.1)

HSP 1 Score: 93.5893 bits (231), Expect = 1.097e-22
Identity = 63/155 (40.65%), Postives = 92/155 (59.35%), Query Frame = 2 
Query:  113 DSQNSYPMLPPKLNETERMVHVQHWINNLPIDVEXXXXXXXXXXXXXXXXLQI--------NVYNQISFGGDVMH--NDSKNKTLTC-SNRLFTESETQLLVDLFKDYFISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKWVGYI 544
            +  +S+P+LPPKL+ETERM HVQ W+N+L  + ES SYAPSAPDSS+     +        N  N + +     H  ND  ++     S RLFT  E ++LV +F+D+F + ICP+  E+R R   T+L   R P S+R K KR+ +  +W+ Y+
Sbjct:    3 EDDDSFPILPPKLHETERMYHVQKWVNSLTWETESNSYAPSAPDSSATDGSHLLNNNSHKGNSGNDLHYFMSSFHQNNDYLHENYQAPSRRLFTNEENRVLVKIFRDHFTAKICPNLPEVRNRIQGTKLGTDRGPISVRNKFKRLQNESQWMNYV 157
The following BLAST results are available for this feature:
BLAST of SMED30031429 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 SMED30031429 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 SMED30031429 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 SMED30031429 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 SMED30031429 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 SMED30031429 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 SMED30031429 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 SMED30031429 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183SGK31.214e-1050.00Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A0R3SI424.431e-1045.16Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
A0A1S8WZ651.055e-948.44Uncharacterized protein (Fragment) OS=Opisthorchis... [more]
A0A564YWJ13.033e-945.16Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
A0A4V3SHA23.421e-948.44Uncharacterized protein OS=Opisthorchis felineus O... [more]
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BLAST of SMED30031429 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 SMED30031429 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 SMED30031429 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 SMED30031429 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 SMED30031429 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 SMED30031429 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000038604.16.090e-93100.00SMESG000038604.1[more]
SMESG000038604.18.995e-85100.00SMESG000038604.1[more]
SMESG000038604.11.974e-42100.00SMESG000038604.1[more]
SMESG000038604.16.932e-35100.00SMESG000038604.1[more]
SMESG000064860.11.097e-2240.65SMESG000064860.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031429 ID=SMED30031429|Name=SMED30031429|organism=Schmidtea mediterranea sexual|type=transcript|length=1170bp
GTAAGTAAACATCATCTATTTGTATATATTAGCAAAAAAAATAATTTCCA
CTACAGATTATATTTATTTTAATAAAGCTAACAATCTAAGCTGAAGGTTT
GCTATGAATTCTGATTCACAAAACAGTTATCCTATGCTTCCTCCAAAGCT
AAATGAAACAGAAAGAATGGTTCATGTACAGCATTGGATAAATAATCTGC
CTATAGATGTGGAATCATGTTCGTATGCGCCATCGGCTCCTGATTCTTCT
TCTGATAGCTGTTTACAAATTAATGTTTACAACCAGATATCATTTGGTGG
GGATGTAATGCATAATGACTCAAAAAATAAAACATTGACGTGTTCTAATC
GATTGTTTACCGAAAGTGAAACTCAACTTTTAGTTGATTTGTTTAAAGAT
TATTTCATTAGTGGTATATGTCCATCTACTGACGAAATTAGAAAGCGAAC
AGGATGTACCGAGTTAGCTCTTTATAGGAATCCAACTAGTCTTCGTGGTA
AAGTCAAACGAATGATCAGTAATCGTAAATGGGTTGGATACATTAGACAC
TCGTGAAGAATCAATATTTATTACCGAAAATGTTGTTGATTGGTTTAGAA
ATTGATACCATTATTATTATGAACTGTTTTTTATTATTACGGTGCAGTTT
GTCAATTGAGAATAAATGTGATTTTCATTTGAAAGATTTCGGGATTATTT
TTATACACTTTAATGTTATTTGTTACTTTGATTCTGAAATTATACCCAAT
TGTTGTTTTTGGGTTATTAATATATTTCCTATGCACAGAATGGTAAATTG
TTGGATGTGGCAAATTTTACTTATGAGAATAAGGACGAATTTGGACACAA
TTTTTTAACTTTACTGGTTATTATAATTTTTAATAACTCTGGCACGAGAA
TCTTGAAGATTTTTGAAGCCTTTCCTTTGTGAAATTATAAATTGTCGAGA
TATCTGTTTTAGCTGACAAAATTATTTGATCAACTTTATTCGGGTCCAAC
GCGTAAATTTTATTAATGTTCCCTGCAGCACTTGTAACATTCTGGGTGAA
CCTCTTCGCCTCTCCAACGATTGTGAAATTGAACCAGGCTATTTTTATGG
TAGAATGAGCTTTGATATTTCATACAGACAAATGGTTGCAGTTATTTTTG
AAAAGGAAATTTTTTTCATT
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protein sequence of SMED30031429-orf-1

>SMED30031429-orf-1 ID=SMED30031429-orf-1|Name=SMED30031429-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=151bp
MNSDSQNSYPMLPPKLNETERMVHVQHWINNLPIDVESCSYAPSAPDSSS
DSCLQINVYNQISFGGDVMHNDSKNKTLTCSNRLFTESETQLLVDLFKDY
FISGICPSTDEIRKRTGCTELALYRNPTSLRGKVKRMISNRKWVGYIRHS
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron