SMED30004487

Overview
NameSMED30004487
Smed IDSMED30004487
Length (bp)809
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 SMED30004487 (SMED30004487) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004487 (SMED30004487) 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 SMED30004487 (SMED30004487) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004487 (SMED30004487) 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




SMED30004487

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
neuronSMED30004487SMESG000012170.1 SMESG000012168.1 dd_Smed_v4_1367_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30004487SMESG000012170.1 SMESG000012168.1 dd_Smed_v4_1367_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30004487SMESG000012170.1 SMESG000012168.1 dd_Smed_v4_1367_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30004487 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005073:4963..5770 -3977
Homology
BLAST of SMED30004487 vs. TrEMBL
Match: A0A3P7P2W1 (Uncharacterized protein OS=Dibothriocephalus latus OX=60516 GN=DILT_LOCUS8117 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 8.381e-8
Identity = 43/138 (31.16%), Postives = 72/138 (52.17%), Query Frame = 1
Query:  175 MNTLSLSLGLIISMFVLLIIAVATPYWHCGNILLDC-----NHYGTWVAAKIFFMLGLVCCAVVLILEILGYACLNYRSHGTMNLVKXXXXXXXXXXXXXXXXXFNSVTNNQWSYMLAVVGMTLGLQVFIIGLMSSSC 573
            M+   ++  L+    V LI+ +ATP W C ++  DC     N     ++     ++GLVC  VV IL++L     + +  G   + +  LL +    LL+ ++++ + T+N WSY LAV     GL V I+G+M+S C
Sbjct:    1 MDLRRITATLLALTIVTLIVGLATPNWDCVSLFEDCIEEGANERVAMISVAALLVIGLVCLTVVFILDVLYLR--SKQLSGVAQVARFCLLYLGAAMLLVAVIVYTAQTHNHWSYFLAVASAAFGLTVAILGVMASRC 136          
BLAST of SMED30004487 vs. TrEMBL
Match: A0A0X3P940 (Uncharacterized protein (Fragment) OS=Schistocephalus solidus OX=70667 GN=TR130023 PE=4 SV=1)

HSP 1 Score: 61.6178 bits (148), Expect = 1.470e-7
Identity = 43/139 (30.94%), Postives = 73/139 (52.52%), Query Frame = 1
Query:  172 NMNTLSLSLGLIISMFVLLIIAVATPYWHCGNILLDC-----NHYGTWVAAKIFFMLGLVCCAVVLILEILGYACLNYRSHGTMNLVKXXXXXXXXXXXXXXXXXFNSVTNNQWSYMLAVVGMTLGLQVFIIGLMSSSC 573
            +M+   ++  L+    V LI+ +ATP W C  +  DC     N     ++     ++GL C  +V IL+++   C  + S G  ++ +  LL +    LL+ ++++ + T+N WSY LAV     GL V I+G+MSS C
Sbjct:   94 SMDLRRVTSALLALTIVTLIVGLATPNWDCVGLFEDCIKEGANEREAMISVAALLVIGLFCLTIVFILDVVSL-CSKHLS-GPAHVARFFLLYLGAALLLVAVIVYTAETHNHWSYFLAVASAAFGLTVAILGVMSSRC 230          
BLAST of SMED30004487 vs. TrEMBL
Match: A0A183SJ36 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS4234 PE=4 SV=1)

HSP 1 Score: 61.6178 bits (148), Expect = 1.635e-7
Identity = 43/139 (30.94%), Postives = 73/139 (52.52%), Query Frame = 1
Query:  172 NMNTLSLSLGLIISMFVLLIIAVATPYWHCGNILLDC-----NHYGTWVAAKIFFMLGLVCCAVVLILEILGYACLNYRSHGTMNLVKXXXXXXXXXXXXXXXXXFNSVTNNQWSYMLAVVGMTLGLQVFIIGLMSSSC 573
            +M+   ++  L+    V LI+ +ATP W C  +  DC     N     ++     ++GL C  +V IL+++   C  + S G  ++ +  LL +    LL+ ++++ + T+N WSY LAV     GL V I+G+MSS C
Sbjct:   94 SMDLRRVTSALLALTIVTLIVGLATPNWDCVGLFEDCIKEGANEREAMISVAALLVIGLFCLTIVFILDVVSL-CSKHLS-GPAHVARFFLLYLGAALLLVAVIVYTAETHNHWSYFLAVASAAFGLTVAILGVMSSRC 230          
BLAST of SMED30004487 vs. TrEMBL
Match: A0A183AUP5 (Uncharacterized protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS10680 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 5.076e-6
Identity = 42/120 (35.00%), Postives = 62/120 (51.67%), Query Frame = 1
Query:  223 LLIIAVATPYWHCGNILLDCN---HYGTWVAAKIFFMLGLVCCAVVLILEILGYACLNYRSHGTMNLVKXXXXXXXXXXXXXXXXXFNSVTNNQWSYMLAVVGMTLGLQVFIIGLMSSSC 573
            L+II +AT  W CG +  +C    H    +A  I  ++G+VC A+V IL+++G     +         + I L +    LLI IL+F     + WSY LA VG    +QV I+ +MSS C
Sbjct:   18 LVIIGLATSSWSCGGLFDNCQRGYHKDAAIAVLILLLIGVVCLAIVFILDLVGLCSDVFVVSAGYITTRFIFLYLGSTVLLIGILVFTGSIGHAWSYFLATVGCVFAMQVAILAIMSSRC 137          
BLAST of SMED30004487 vs. TrEMBL
Match: A0A0R3SQQ3 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS7422 PE=4 SV=1)

HSP 1 Score: 55.0694 bits (131), Expect = 8.324e-6
Identity = 46/136 (33.82%), Postives = 68/136 (50.00%), Query Frame = 1
Query:  196 LGLIISMFVLLIIAVAT--PYWHCGNILLDCNHYGTWVAAKIFFMLGLVCC--------AVVLILEILGYACLNYRSHGTMNLVKXXXXXXXXXXXXXXXXXFNSVTNNQWSYMLAVVGMTLGLQVFIIGLMSSSC 573
            L LI+ +F L  + VAT  P WHCG++   C H G   A +   MLG+ CC        A+V I++ + + C   RS    N+V+L LL I     +  ++L+    N  WSY LA  G     QV ++ L+ + C
Sbjct:    6 LTLIVLVFALAALTVATVLPQWHCGSLFEKCTHDG---AGRRDVMLGVACCLVIGVTMLAIVCIIDFI-HICSKTRSK-VENVVRLALLYIGSILCVTAVILYTVEINQSWSYFLATCGAVFATQVCLLTLIYARC 136          
BLAST of SMED30004487 vs. Planmine SMEST
Match: SMESG000012170.1 (SMESG000012170.1)

HSP 1 Score: 223.016 bits (567), Expect = 5.294e-74
Identity = 132/133 (99.25%), Postives = 133/133 (100.00%), Query Frame = 1
Query:  175 MNTLSLSLGLIISMFVLLIIAVATPYWHCGNILLDCNHYGTWVAAKIFFMLGLVCCAVVLILEILGYACLNYRSHGTMNLVKXXXXXXXXXXXXXXXXXFNSVTNNQWSYMLAVVGMTLGLQVFIIGLMSSSC 573
            MNTLSLSLGLIISMFVLLIIAVATPYWHCGNILLDCNHYGTWVAAKIFFMLGLVCCAVVLILEILGYACLNYRSHGTMNLVKLILLGISVGSLLICILLFNSVT+NQWSYMLAVVGMTLGLQVFIIGLMSSSC
Sbjct:    1 MNTLSLSLGLIISMFVLLIIAVATPYWHCGNILLDCNHYGTWVAAKIFFMLGLVCCAVVLILEILGYACLNYRSHGTMNLVKLILLGISVGSLLICILLFNSVTSNQWSYMLAVVGMTLGLQVFIIGLMSSSC 133          
BLAST of SMED30004487 vs. Planmine SMEST
Match: SMESG000012166.1 (SMESG000012166.1)

HSP 1 Score: 142.51 bits (358), Expect = 2.568e-42
Identity = 86/133 (64.66%), Postives = 107/133 (80.45%), Query Frame = 1
Query:  175 MNTLSLSLGLIISMFVLLIIAVATPYWHCGNILLDCNHYGTWVAAKIFFMLGLVCCAVVLILEILGYACLNYRSHGTMNLVKXXXXXXXXXXXXXXXXXFNSVTNNQWSYMLAVVGMTLGLQVFIIGLMSSSC 573
            MNT +LSLGLIIS F+LL+IA+ATPYW+CGN+L DCN  G  +A KIFFMLGLV  AVVLILEILG   + YR + ++NL +LILLGI + SLLIC+L+F S+  + WSYML V+ +TLGLQV IIG+M+SSC
Sbjct:    1 MNTSNLSLGLIISTFILLVIAIATPYWNCGNLLTDCNE-GKDIAVKIFFMLGLVSIAVVLILEILGIVSITYRGNSSINLARLILLGIGICSLLICVLVFTSIRGHNWSYMLTVIALTLGLQVLIIGMMTSSC 132          
BLAST of SMED30004487 vs. Planmine SMEST
Match: SMESG000012168.1 (SMESG000012168.1)

HSP 1 Score: 99.3673 bits (246), Expect = 9.130e-26
Identity = 78/133 (58.65%), Postives = 101/133 (75.94%), Query Frame = 1
Query:  175 MNTLSLSLGLIISMFVLLIIAVATPYWHCGNILLDCNHYGTWVAAKIFFMLGLVCCAVVLILEILGYACLNYRSHGTMNLVKXXXXXXXXXXXXXXXXXFNSVTNNQWSYMLAVVGMTLGLQVFIIGLMSSSC 573
            MNT  LSL L+IS   LLI A+  PYWHCGNIL DCN+    V AKIFF+LGLVC  VVL+LE++ +  ++Y  + ++NLV+LI+LGI+VGSLL+CIL++ S   NQWSYM  V+ MTL +Q F+IG+MSSSC
Sbjct:    1 MNTNRLSLVLVISTVSLLITAMILPYWHCGNILSDCNYDAGLVVAKIFFILGLVCFVVVLVLELIQFCTISYYGNASLNLVRLIMLGIAVGSLLMCILIYTSNIVNQWSYMCTVIAMTLAVQAFVIGIMSSSC 133          
BLAST of SMED30004487 vs. Planmine SMEST
Match: SMESG000011804.1 (SMESG000011804.1)

HSP 1 Score: 48.1358 bits (113), Expect = 8.013e-7
Identity = 42/135 (31.11%), Postives = 74/135 (54.81%), Query Frame = 1
Query:  175 MNTLSLSLGLIISMFVLLIIAVATPYWHCGNILLDCNHYGT--WVAAKIFFMLGLVCCAVVLILEILGYACLNYRSHGTMNLVKXXXXXXXXXXXXXXXXXFNSVTNNQWSYMLAVVGMTLGLQVFIIGLMSSSC 573
            ++++ ++L  +    VLLI A ATPYW CG +  DC  +     ++  I F LG+    VV +L+ +         + T N V+L+LL + VG ++  + +  S     WS+++A+VG TL +QV ++ L + +C
Sbjct:    2 IDSVRITLVFLFVSIVLLICAAATPYWGCGYLYTDCIQHDKVQGLSVMILFTLGICFLIVVAVLDFVNCCNGTLLLNVTTNQVRLVLLFLGVGCIVSAVCIHASYRAPIWSFLMAIVGGTLLVQVIVLALNTCTC 136          
The following BLAST results are available for this feature:
BLAST of SMED30004487 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 SMED30004487 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 SMED30004487 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 SMED30004487 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 SMED30004487 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 SMED30004487 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 SMED30004487 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 SMED30004487 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3P7P2W18.381e-831.16Uncharacterized protein OS=Dibothriocephalus latus... [more]
A0A0X3P9401.470e-730.94Uncharacterized protein (Fragment) OS=Schistocepha... [more]
A0A183SJ361.635e-730.94Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A183AUP55.076e-635.00Uncharacterized protein OS=Echinostoma caproni OX=... [more]
A0A0R3SQQ38.324e-633.82Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
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BLAST of SMED30004487 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 SMED30004487 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 SMED30004487 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 SMED30004487 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 SMED30004487 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 SMED30004487 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000012170.15.294e-7499.25SMESG000012170.1[more]
SMESG000012166.12.568e-4264.66SMESG000012166.1[more]
SMESG000012168.19.130e-2658.65SMESG000012168.1[more]
SMESG000011804.18.013e-731.11SMESG000011804.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004487 ID=SMED30004487|Name=SMED30004487|organism=Schmidtea mediterranea sexual|type=transcript|length=809bp
GCATGCTATTCGGTTACAGAATTCGTAGAACTGACTTGCTGGAAATACCC
TAAGTCATCGCATGCCGAACGTGACAAATGTGGAGATACATGCATATTTT
ATTTATATTCCAGTTTAAATAAGATAATGTCGTAATAAAATAGTCATTTT
AACCTGAAAATTTAGAAACCAAACATGAACACTCTCAGTTTATCTCTGGG
ATTAATAATCTCCATGTTTGTACTTTTAATAATTGCCGTAGCGACTCCCT
ATTGGCATTGTGGAAATATCCTTCTAGACTGCAACCATTATGGAACCTGG
GTCGCTGCTAAAATCTTCTTCATGCTTGGATTGGTTTGTTGTGCAGTGGT
TTTGATTTTGGAAATACTCGGATACGCCTGTCTCAATTATCGGTCTCATG
GCACCATGAATTTGGTGAAATTGATTCTGTTAGGGATCTCGGTTGGCAGT
TTACTCATCTGTATATTATTGTTCAATTCAGTTACAAATAACCAATGGTC
ATATATGTTGGCCGTTGTCGGCATGACTCTTGGATTGCAGGTGTTCATTA
TAGGTTTGATGAGTAGCAGCTGTACCATGACCACACGAACGACTCACGTC
GTAGTGACTCGTTAAGCAAAAGCAATTTTATCTTGATTTAAAATTTGTTT
AAATGAACCAATTTAGTCAATATAACCCTCGGATTAGTTCTTATATAGCA
TGATGAATTCAGCTGCACAATTAATAGACATCCAAAAGTGCATCGGTGGT
TCCTGTTTGTAATATCAATTATTTCTTTTTATTAATAATAAATTTGATTA
ATTTTCAAT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 81..103
NoneNo IPR availableTMHMMTMhelixcoord: 47..69
NoneNo IPR availableTMHMMTMhelixcoord: 5..27
NoneNo IPR availableTMHMMTMhelixcoord: 108..130