SMED30020784

Overview
NameSMED30020784
Smed IDSMED30020784
Length (bp)1460
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 SMED30020784 (SMED30020784) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020784 (SMED30020784) 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 SMED30020784 (SMED30020784) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020784 (SMED30020784) 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




SMED30020784

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30020784SMESG000011782.1 Contig1076GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30020784SMESG000011782.1 Contig1076GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30020784SMESG000011782.1 Contig1076GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30020784SMESG000011782.1 Contig1076GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
parapharyngeal regionSMED30020784SMESG000011782.1 SmedASXL_009836SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30020784SMESG000011782.1 dd_Smed_v4_10359_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
gutSMED30020784SMESG000011782.1 dd_Smed_v4_10359_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30020784SMESG000011782.1 dd_Smed_v4_10359_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
gutSMED30020784SMESG000011782.1 Contig32583newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30020784SMESG000011782.1 Contig32583uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020784 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001113:32239..40607 -7116
Homology
BLAST of SMED30020784 vs. Planmine SMEST
Match: SMESG000011782.1 (SMESG000011782.1)

HSP 1 Score: 574.318 bits (1479), Expect = 0.000e+0
Identity = 353/353 (100.00%), Postives = 353/353 (100.00%), Query Frame = 1
Query:  205 MLLLQFLIAFIISMCFLIDSASTQCKLKPIFGKICSNTDYVPKQIIIQSISRFVNIRFISMRNEMDLRIPPNYHNTSDGDYAGFSIIKSCVKSIEEHFFLKLDKNKNTLNRIEFLKVSCLTSLLTKSFIGIGNSIQSLKFNELPDLVNIDGDVFNSFTKLQTLEITKTKLIRVPDTMXXXXXXXXXXXXXXXXXXXMPFLPRDRPELVNDFQGFGNPFYCECSLMKFIDIIRXXXXXXXXXXXXXYTCETPEHLSEVNLIDAGDLCITTTKSTEPVKILSQTVTPAAIKIELIAAVAGSXXXXXXXXXXXXXXXXXXXXXXXXXXYSEGSPSKIIFQDDDYNEPFIKEKPRKV 1263
            MLLLQFLIAFIISMCFLIDSASTQCKLKPIFGKICSNTDYVPKQIIIQSISRFVNIRFISMRNEMDLRIPPNYHNTSDGDYAGFSIIKSCVKSIEEHFFLKLDKNKNTLNRIEFLKVSCLTSLLTKSFIGIGNSIQSLKFNELPDLVNIDGDVFNSFTKLQTLEITKTKLIRVPDTMINVLPNLKILKINNNKLTKMPFLPRDRPELVNDFQGFGNPFYCECSLMKFIDIIRNNLKNPNNLKNENYTCETPEHLSEVNLIDAGDLCITTTKSTEPVKILSQTVTPAAIKIELIAAVAGSVLVVVLVIIIVLVCKKKKKESKRKILYSEGSPSKIIFQDDDYNEPFIKEKPRKV
Sbjct:    1 MLLLQFLIAFIISMCFLIDSASTQCKLKPIFGKICSNTDYVPKQIIIQSISRFVNIRFISMRNEMDLRIPPNYHNTSDGDYAGFSIIKSCVKSIEEHFFLKLDKNKNTLNRIEFLKVSCLTSLLTKSFIGIGNSIQSLKFNELPDLVNIDGDVFNSFTKLQTLEITKTKLIRVPDTMINVLPNLKILKINNNKLTKMPFLPRDRPELVNDFQGFGNPFYCECSLMKFIDIIRNNLKNPNNLKNENYTCETPEHLSEVNLIDAGDLCITTTKSTEPVKILSQTVTPAAIKIELIAAVAGSVLVVVLVIIIVLVCKKKKKESKRKILYSEGSPSKIIFQDDDYNEPFIKEKPRKV 353          
BLAST of SMED30020784 vs. Planmine SMEST
Match: SMESG000067732.1 (SMESG000067732.1)

HSP 1 Score: 59.3066 bits (142), Expect = 1.963e-9
Identity = 56/253 (22.13%), Postives = 104/253 (41.11%), Query Frame = 1
Query:  274 QCKLKPIFGKICSNTDYVPKQIIIQSISRFVNIRFISMRNEMDLRIPPNYHNTSDGDYAGFSII---KSCVKSIEEHFFLKLDKNKNTLNRIEFLKVSCLTSLLTKSFIGIGNSIQSLKFNELPDLVNIDGDVFNSFTKLQTLEITKTKLIRVPDTMXXXXXXXXXXXXXXXXXXXMPFLPRDRPELVNDFQGFGNPFYCECSLMKFIDIIRXXXXXXXXXXXXXYTCETPEHLSEVNLIDAGDLCITTTKST 1023
            +C+ K   G IC+  D+  + ++I S     ++   ++ N + L  P         DY  FS I     C+  ++E FF +L +    L +I  L V+C   +    F G+  +    K  ELP+      ++F S + L  L+ +   L+R                        +PF P  +P  + DFQ FGN + C+C +  +++ + +     +        C +P  +  + + D  D+C +   S+
Sbjct:    2 ECQFKIYVGMICTGNDFNTQMLLISSNVAHNSLFLFNISNSIKLTTPKKDFKV---DYIKFSYITIKNICIVKLDEGFFGELGQ----LMKIHLLNVTCFKGIREIHFKGLDET----KLKELPE------NLF-SLSHLIKLDFSWNYLVR------------------------LPFYPLVKPLFLGDFQIFGNYWMCDCGMKIYVEFVTDPRFVQS-------KCFSPIRVRGLRMCDVKDMCGSYEASS 205          
The following BLAST results are available for this feature:
BLAST of SMED30020784 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 SMED30020784 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 SMED30020784 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 SMED30020784 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 SMED30020784 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 SMED30020784 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 SMED30020784 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 SMED30020784 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020784 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 SMED30020784 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 SMED30020784 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 SMED30020784 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 SMED30020784 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 SMED30020784 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000011782.10.000e+0100.00SMESG000011782.1[more]
SMESG000067732.11.963e-922.13SMESG000067732.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020784 ID=SMED30020784|Name=SMED30020784|organism=Schmidtea mediterranea sexual|type=transcript|length=1460bp
CCGATTTCGGTTGCCGAGGTTGTGTAAACGTCAAAAACAAGGTTAACGAA
CTTAATTTGAACAGTCAAATACAAATATTAAGTATTGATACTGTTGTTGA
AATCACAATTAAGTGGTCTCACTTTACAGCTTTCTCTCTCTCTCTCTATC
TCTAGCTTTCTCGCTTTTATATCAGGTTGAAATTGGTTTTGTGTATTACG
GAAAATGCTACTCTTACAATTTTTAATTGCCTTTATTATTTCTATGTGTT
TTTTAATTGATTCTGCGTCGACTCAATGTAAACTCAAACCAATTTTCGGA
AAAATTTGTTCTAATACCGATTATGTGCCAAAACAAATAATAATTCAATC
CATTTCTAGGTTTGTCAACATTCGTTTCATCAGCATGAGAAACGAGATGG
ACCTGAGGATTCCGCCAAATTACCACAACACAAGTGACGGAGACTATGCG
GGATTTAGTATCATTAAATCGTGCGTCAAATCAATAGAAGAGCACTTTTT
TCTAAAGCTCGATAAAAACAAAAACACATTAAATCGAATCGAATTTCTCA
AAGTCAGTTGTCTTACGAGCTTGTTGACAAAATCTTTCATTGGAATCGGA
AATTCAATTCAGTCGCTAAAATTTAACGAATTGCCCGATTTGGTCAACAT
AGATGGGGATGTTTTCAATTCATTTACCAAATTGCAAACTCTGGAAATAA
CTAAAACCAAACTTATCAGGGTACCCGACACAATGATAAATGTCTTGCCG
AATTTAAAAATTTTGAAGATTAACAATAATAAATTGACAAAAATGCCTTT
CCTTCCTCGGGATAGACCAGAATTAGTGAATGATTTCCAAGGCTTTGGGA
ACCCCTTTTACTGTGAATGCTCACTCATGAAATTTATCGACATTATAAGA
AACAATTTGAAAAACCCTAACAACCTCAAAAATGAAAACTATACATGTGA
AACTCCAGAACACCTTTCCGAGGTAAACTTGATTGATGCAGGAGATCTCT
GTATCACAACAACAAAATCAACAGAACCTGTAAAAATATTAAGTCAAACA
GTGACCCCAGCAGCAATAAAGATCGAACTAATAGCAGCTGTAGCAGGTTC
AGTGTTAGTAGTTGTTTTAGTAATTATTATAGTGCTTGTTTGCAAAAAAA
AGAAAAAAGAATCTAAAAGAAAAATCTTGTACTCGGAAGGCTCTCCTTCA
AAGATTATATTCCAAGATGATGATTACAATGAGCCGTTTATTAAAGAGAA
ACCTCGCAAAGTTTGAATTCGAAATTCTAAATAAAAAGTAAAAAAACCCG
GAAGTGTCGGTTCATAGCTAACTTAGAATTTAACTTTTTTGTATAACATT
GTAGAGATATTTTTATGTTTTTTACGGTTCTCTCTCTCCAATTTTTTTGT
ATGTATATTGTTTTTATTGTCACTGAATATTATTGTTATTATTAAATCTG
ATTTTTGAAC
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protein sequence of SMED30020784-orf-1

>SMED30020784-orf-1 ID=SMED30020784-orf-1|Name=SMED30020784-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=354bp
MLLLQFLIAFIISMCFLIDSASTQCKLKPIFGKICSNTDYVPKQIIIQSI
SRFVNIRFISMRNEMDLRIPPNYHNTSDGDYAGFSIIKSCVKSIEEHFFL
KLDKNKNTLNRIEFLKVSCLTSLLTKSFIGIGNSIQSLKFNELPDLVNID
GDVFNSFTKLQTLEITKTKLIRVPDTMINVLPNLKILKINNNKLTKMPFL
PRDRPELVNDFQGFGNPFYCECSLMKFIDIIRNNLKNPNNLKNENYTCET
PEHLSEVNLIDAGDLCITTTKSTEPVKILSQTVTPAAIKIELIAAVAGSV
LVVVLVIIIVLVCKKKKKESKRKILYSEGSPSKIIFQDDDYNEPFIKEKP
RKV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000420parapharyngeal region
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR032675LRR_dom_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR032675Leucine-rich repeat domain superfamilyGENE3DG3DSA:3.80.10.10coord: 39..264
e-value: 3.6E-17
score: 63.3
NoneNo IPR availablePANTHERPTHR46473FAMILY NOT NAMEDcoord: 125..320
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..23
score: 0.739
NoneNo IPR availableSUPERFAMILYSSF52058L domain-likecoord: 98..262
NoneNo IPR availableTMHMMTMhelixcoord: 290..312