SMED30024730

Overview
NameSMED30024730
Smed IDSMED30024730
Length (bp)1618
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 SMED30024730 (SMED30024730) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024730 (SMED30024730) 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 SMED30024730 (SMED30024730) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024730 (SMED30024730) 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



SMED30024730

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
tail regionSMED30024730SMESG000047702.1 SmedASXL_014906SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30024730SMESG000047702.1 dd_Smed_v4_15765_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30024730SMESG000047702.1 dd_Smed_v4_15765_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30024730SMESG000047702.1 dd_Smed_v4_15765_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30024730SMESG000047702.1 dd_Smed_v6_15765_0_1dd_Smed_v6PMID:30399335
Ross et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30024730SMESG000047702.1 dd_Smed_v6_15765_0_1dd_Smed_v6PMID:30399335
Ross et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30024730SMESG000047702.1 dd_Smed_v4_15765_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30024730SMESG000047702.1 dd_Smed_v4_15765_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
Alignments
SMED30024730 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011962:819..13501 +6308
Homology
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BLAST of SMED30024730 vs. TrEMBL
Match: A0A1S3HT32 (CAP-Gly domain-containing linker protein 1 isoform X3 OS=Lingula unguis OX=7574 GN=LOC106157925 PE=4 SV=1)

HSP 1 Score: 65.4698 bits (158), Expect = 1.652e-7
Identity = 89/418 (21.29%), Postives = 193/418 (46.17%), Query Frame = 2 
Query:   80 LINNRSVMINYVIVDENIIALCNEKNIVSADNLSKLKNATTNQVKIDCIIESLTMKKPKYFEDFCEILVLSGFPIIAEILHG-TTSSEVSVDLN-------DIWEEIPNLKKTITQKEKDLLFKYINSKIKEENIKNLL-SQPKETQRKTSIARLNQVEQSWKFQREIKSKEVEKDQLKIQLTAXXXXXXXXXXXXNVVIEEHKKRKQQQGEELVIAAKFNTANDKEIQRIERSL----NLFKNMVTKMSSKIRIILQSSSDSHSRLIRESSESNLKKFDIDKQLEIFEKLFETMANLYNNLVEEMTIFENLKTEIQSVKQRFQLNSINDPKENLTTVMGNYEMAINNKIGQLYEQIEMQESFIFGILSPENVPEKYKHIQIESSERNEFLNIINELKKKIQYLESVVAVKDKELKSF 1294
            L  NR ++   +I  +       ++N+++   LS + N      +I+ +I+ L ++    F  FC++L ++G  ++A+ L     S+  S D         D++   P+L K ++  EK +L  YI  + +E  +  L   Q +E Q     A+  Q+E+SW+    ++ K+V   +L+ +    +E L EK  E   ++   ++ K++   +L     FN+AND  ++R++  +        +M   M  K+R +   +         E +  +++  D +KQ  + EK   +  + ++ L      +E+   E Q V + F + + + P       M N+  + ++++ +L++++E +E+ I        V ++   +Q E +          +L+K I+ L + +A +DK+++  
Sbjct:    9 LDENRVLLARNIIPTKEFYDRLQKQNVLTESMLSNIANVVNRDAQINSMIDMLLVRVTAAFHKFCDVLQVTGHHLLADHLRNEALSASESKDFPGGETPEPDVFRRFPSLNKALSDVEKQVLDGYIKEREREAALTALWKGQSREKQIALD-AKQKQMEESWEHMEVMQKKDVLIHRLEDECQKAQEALQEKTAEYMKLLRNAEEAKEKHKLQLDTQMNFNSANDSTLRRLQERITEMETALNDMDAYMEEKLRKVEPPT---------EEAPLDIQHLD-NKQ--VREKRVRSFLDHFDRLYLISRKYEDALQERQDVLKLFAIEADSKP---FYAHMRNFHDSNSDRLARLFKELEHRETRI------SEVQDEVAKVQGEKA----------DLEKTIEDLNAQLAERDKQIRDL 394
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BLAST of SMED30024730 vs. TrEMBL
Match: V4BEU0 (CARD domain-containing protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_170847 PE=4 SV=1)

HSP 1 Score: 61.6178 bits (148), Expect = 3.303e-6
Identity = 51/241 (21.16%), Postives = 117/241 (48.55%), Query Frame = 2 
Query:   80 LINNRSVMINYVIVDENIIALCNEKNIVSADNLSKLKNATTNQVKIDCIIESLTMKKPKYFEDFCEILVLSGFPIIAEILHGTTSSEVSVDLNDIWEEIPNLKKTITQKEKDLLFKYINSKIKEENIKNLLSQPKETQRKTSIARLNQVEQSWKFQREIKSKEVEKDQLKIQLTAXXXXXXXXXXXXNVVIEEHKKRKQQQGEELVIAAKFNTANDKEIQRIERSLNLFKNMVTKMSSKIR 802
            L  +R+ +I  +I ++ +  L   + +V+   L+ +    +   K+  ++E L +K  + +  FC +L ++G   +A+ L    ++E + ++ D+ + +P L K +   E+ L+  Y+  KI+ E +K +       + K   A+L Q+E     + + K  + + ++LK  L    E+ +  + ++N +  E    +++  E+L    KFN AN+  ++++          +T++   IR
Sbjct:    9 LQTHRNFVIKNIIWNDQLAELLKSQGLVTDSILTDINKQESRDEKVKVLLERLVLKAGQAYHKFCNVLQVTGHYFLADFLRDEETNE-TANVKDLVKRLPFLGKVLKDNERKLVESYVIEKIQSETLKYIWKNEAREKDKALDAKLKQLETEVLMKEKSKDADSKINELKGTLMTASEECVVLKAQINALKAEIPAIRKEHQEDLNKQVKFNMANENSLKKVTEKFEHADKAITRIRLMIR 248
[Close]
BLAST of SMED30024730 vs. Planmine SMEST
Match: SMESG000047702.1 (SMESG000047702.1)

HSP 1 Score: 929.087 bits (2400), Expect = 0.000e+0
Identity = 496/504 (98.41%), Postives = 501/504 (99.40%), Query Frame = 2 
Query:   29 MNISSTLKVLGQNYCDNLINNRSVMINYVIVDENIIALCNEKNIVSADNLSKLKNATTNQVKIDCIIESLTMKKPKYFEDFCEILVLSGFPIIAEILHGTTSSEVSVDLNDIWEEIPNLKKTITQKEKDLLFKYINSKIKEENIKNLLSQPKETQRKTSIARLNQVEQSWKFQREIKSKEVEKDQLKIQLTAXXXXXXXXXXXXNVVIEEHKKRKQQQGEELVIAAKFNTANDKEIQRIERSLNLFKNMVTKMSSKIRIILQSSSDSHSRLIRESSESNLKKFDIDKQLEIFEKLFETMANLYNNLVEEMTIFENLKTEIQSVKQRFQLNSINDPKENLTTVMGNYEMAINNKIGQLYEQIEMQESFIFGILSPENVPEKYKHIQIESSERNEFLNIINELKKKIQYLESVVAVKDKELKSFSQSKFKXXXXXXXXXXXXXXXXHKAETDISSTGKERKPNFQRVLPNIPYSYSSKHTQRVSNGNLNIKPKKTNFLKTNVVSFI 1540
            MNISSTLKVLGQNYCDNLINNRSVMINYVIVDENIIALCNEKNIVSADNLSKLKNATTNQVKIDCIIESLTMKKPKYFEDFCEILVLSG+PIIAEILHGTTSS VSVDLNDIWEEIPNLKKTITQKEKDLLFKYIN KIKEENIKNLLSQPKETQRKTSIARLNQVEQSWKFQREIKSKEVEKDQLKIQLTAIEE+LIEKQKELNVVIEEHKKRKQQQGEELVIAAKFNTANDKEIQRIERSL+LFKNMVTKMSSKIRIILQSSSDSHSRLIRESSESNLKKFDIDKQLEIFEKLFETMANLYNNLVEEMTIFENLKTEIQSVKQRFQ+NSINDPK NLTTVMGNYEMAINNKIGQLYEQIEMQESFIFGILSPENVPEKYKHIQIESSERNEFLNIINELKKKIQYLESVVAVKDKELKSFSQSKFKTNAIIEIIQEETNETNHKAETDISSTGKERKPNFQRVLPNIPYSYSSKHTQRVSNGNLN+KPKKTNFLKTNVVSFI
Sbjct:    1 MNISSTLKVLGQNYCDNLINNRSVMINYVIVDENIIALCNEKNIVSADNLSKLKNATTNQVKIDCIIESLTMKKPKYFEDFCEILVLSGYPIIAEILHGTTSSGVSVDLNDIWEEIPNLKKTITQKEKDLLFKYINDKIKEENIKNLLSQPKETQRKTSIARLNQVEQSWKFQREIKSKEVEKDQLKIQLTAIEERLIEKQKELNVVIEEHKKRKQQQGEELVIAAKFNTANDKEIQRIERSLSLFKNMVTKMSSKIRIILQSSSDSHSRLIRESSESNLKKFDIDKQLEIFEKLFETMANLYNNLVEEMTIFENLKTEIQSVKQRFQVNSINDPKANLTTVMGNYEMAINNKIGQLYEQIEMQESFIFGILSPENVPEKYKHIQIESSERNEFLNIINELKKKIQYLESVVAVKDKELKSFSQSKFKTNAIIEIIQEETNETNHKAETDISSTGKERKPNFQRVLPNIPYSYSSKHTQRVSNGNLNLKPKKTNFLKTNVVSFI 504
The following BLAST results are available for this feature:
BLAST of SMED30024730 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 SMED30024730 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 SMED30024730 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 SMED30024730 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 SMED30024730 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 SMED30024730 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 SMED30024730 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 SMED30024730 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A1S3HT321.652e-721.29CAP-Gly domain-containing linker protein 1 isoform... [more]
V4BEU03.303e-621.16CARD domain-containing protein OS=Lottia gigantea ... [more]
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BLAST of SMED30024730 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 SMED30024730 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 SMED30024730 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 SMED30024730 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 SMED30024730 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 SMED30024730 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000047702.10.000e+098.41SMESG000047702.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024730 ID=SMED30024730|Name=SMED30024730|organism=Schmidtea mediterranea sexual|type=transcript|length=1618bp
ATTTGAGTGTTAAACTTACTCTTATCTGATGAACATTTCGAGCACGTTGA
AGGTATTGGGTCAGAACTATTGCGACAATCTGATCAACAACCGATCAGTG
ATGATCAATTATGTCATAGTTGATGAAAATATTATTGCTTTGTGCAATGA
GAAGAACATCGTTTCAGCGGATAATTTATCTAAATTAAAGAATGCAACTA
CAAATCAAGTAAAAATTGACTGCATTATTGAGTCTTTGACAATGAAGAAA
CCCAAATATTTTGAAGATTTTTGTGAAATTTTGGTTCTTTCTGGTTTTCC
AATAATTGCAGAAATTTTGCATGGAACAACATCTTCTGAAGTTTCAGTAG
ATTTGAATGATATCTGGGAGGAAATACCAAATTTAAAGAAAACAATAACT
CAAAAAGAGAAAGATCTTCTGTTCAAATACATAAATAGTAAAATAAAAGA
AGAAAATATTAAAAATCTTTTAAGTCAACCAAAGGAAACTCAAAGGAAAA
CTTCAATAGCTCGTCTAAACCAAGTTGAGCAATCATGGAAATTTCAAAGA
GAAATCAAAAGTAAAGAAGTTGAAAAAGATCAGCTGAAAATACAATTGAC
TGCGATTGAAGAAAAATTGATAGAAAAGCAAAAGGAACTTAATGTAGTAA
TTGAAGAACATAAAAAGCGAAAACAACAACAGGGAGAAGAATTGGTAATA
GCTGCCAAGTTTAATACGGCCAACGACAAAGAAATTCAAAGAATAGAGCG
TTCACTCAATCTGTTTAAAAATATGGTTACTAAAATGTCCTCTAAAATCC
GAATCATTCTACAAAGTTCATCTGATTCGCATTCTCGTTTAATCCGAGAA
TCATCTGAATCTAACTTGAAAAAGTTCGACATAGATAAGCAGTTGGAGAT
CTTCGAAAAGTTATTTGAAACTATGGCCAATTTATATAATAACCTGGTTG
AAGAAATGACGATTTTTGAAAATTTGAAAACGGAAATTCAATCAGTAAAA
CAAAGATTTCAATTAAATTCTATCAATGATCCAAAAGAAAATTTGACAAC
AGTCATGGGAAATTATGAAATGGCCATAAATAATAAAATTGGTCAACTTT
ATGAACAGATAGAAATGCAAGAAAGTTTTATTTTTGGCATTTTATCGCCG
GAAAATGTCCCAGAAAAATATAAACATATTCAAATTGAATCTAGTGAAAG
AAATGAATTTTTGAACATAATAAATGAATTGAAAAAGAAAATCCAGTACC
TGGAGTCAGTGGTCGCTGTCAAAGATAAAGAATTGAAAAGTTTCTCTCAA
TCGAAATTCAAAACTAATGCAATCATTGAAATTATTCAGGAAGAAACGAA
TGAGACGAATCATAAAGCGGAAACGGATATTTCCTCTACCGGAAAAGAAA
GGAAACCAAATTTTCAGAGAGTTCTTCCGAATATTCCTTATAGCTATTCA
TCAAAACATACACAAAGAGTATCAAATGGTAATTTGAACATAAAACCTAA
AAAGACAAACTTTTTGAAAACTAATGTTGTGAGTTTTATATGAATTTTAT
TTTTACACGGATTGAAGTTTTATTTTTTTGAGATTAAAAAGTTTTAACAA
GTTTTTTGCAATTTTGTG
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protein sequence of SMED30024730-orf-1

>SMED30024730-orf-1 ID=SMED30024730-orf-1|Name=SMED30024730-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=505bp
MNISSTLKVLGQNYCDNLINNRSVMINYVIVDENIIALCNEKNIVSADNL
SKLKNATTNQVKIDCIIESLTMKKPKYFEDFCEILVLSGFPIIAEILHGT
TSSEVSVDLNDIWEEIPNLKKTITQKEKDLLFKYINSKIKEENIKNLLSQ
PKETQRKTSIARLNQVEQSWKFQREIKSKEVEKDQLKIQLTAIEEKLIEK
QKELNVVIEEHKKRKQQQGEELVIAAKFNTANDKEIQRIERSLNLFKNMV
TKMSSKIRIILQSSSDSHSRLIRESSESNLKKFDIDKQLEIFEKLFETMA
NLYNNLVEEMTIFENLKTEIQSVKQRFQLNSINDPKENLTTVMGNYEMAI
NNKIGQLYEQIEMQESFIFGILSPENVPEKYKHIQIESSERNEFLNIINE
LKKKIQYLESVVAVKDKELKSFSQSKFKTNAIIEIIQEETNETNHKAETD
ISSTGKERKPNFQRVLPNIPYSYSSKHTQRVSNGNLNIKPKKTNFLKTNV
VSFI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000096ventral epidermis
PLANA:0000099neuron
PLANA:0000421tail
PLANA:0002032epidermal cell
PLANA:0002056medial muscle cell
Vocabulary: INTERPRO
TermDefinition
IPR011029DEATH-like_dom_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 176..214
NoneNo IPR availableGENE3DG3DSA:1.10.533.10coord: 12..104
e-value: 1.0E-8
score: 37.2
NoneNo IPR availableCDDcd01671CARDcoord: 18..97
e-value: 9.99665E-5
score: 38.6517
IPR011029Death-like domain superfamilySUPERFAMILYSSF47986DEATH domaincoord: 11..100