SMED30014090

Overview
NameSMED30014090
Smed IDSMED30014090
Length (bp)1425
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 SMED30014090 (SMED30014090) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014090 (SMED30014090) 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 SMED30014090 (SMED30014090) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014090 (SMED30014090) 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




SMED30014090

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30014090SMESG000012851.1 SmedASXL_008130SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
neuronSMED30014090SMESG000012851.1 dd_Smed_v4_22852_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neuronSMED30014090SMESG000012851.1 dd_Smed_v4_29680_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30014090SMESG000012851.1 dd_Smed_v6_29680_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
headSMED30014090SMESG000012851.1 dd_Smed_v6_22852_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
headSMED30014090SMESG000012851.1 OX_Smed_1.0.07190ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30014090 vs. TrEMBL
Match: R7UAT1 (Uncharacterized protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_227127 PE=4 SV=1)

HSP 1 Score: 68.9366 bits (167), Expect = 5.878e-9
Identity = 39/140 (27.86%), Postives = 78/140 (55.71%), Query Frame = 3
Query:  867 SHDLTDGNLIIFKLLAFYDRQTLRDIFEVYVQKYKKDIVPDIENSAPESYLRDLLVLSVQILRSDSLYFANEIHNLLKSTDEDSAKNYYLMFYLMTRN----EESITQIKKVYRNHYFESLSDDIRSMVTDPLLQNILVK 1274
            +++L +G+ +   ++       L DIFE Y++  ++D+V +I    P+ ++RD       I  + SL++A +I  LL  T  D   N  L++ +++ +    ++ + ++K+ Y+  YFESL+ DIR    +P +Q +L+K
Sbjct:  194 TNNLFEGDKVFPNIIKTQPASKLADIFEFYLKLCQRDMVVEIHKYYPDGHIRDCYATIASIFHNPSLHYAKKIKRLLPDTYRDGHMN--LLYTVLSLSQKVFQKEVVRLKQTYQATYFESLARDIREESPEPFMQRVLLK 331          
BLAST of SMED30014090 vs. TrEMBL
Match: A0A1S3IH54 (uncharacterized protein LOC106164243 OS=Lingula unguis OX=7574 GN=LOC106164243 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 9.188e-6
Identity = 38/146 (26.03%), Postives = 78/146 (53.42%), Query Frame = 3
Query:  858 SIISHDLTDGNLIIFKLLAFYDRQTLRDIFEVYVQKYKKDIVPDIENSAPESYL---RDLLVLSVQILRSDSLYFANEIHNLLKSTDEDSAKNYYLMFYLMTRNEESITQIKKVYRNHYFESLSDDIRSMVTDPLLQNILVKALAR 1286
            ++ S +L  G+ + FKLL+   R+  +++FE Y+++ ++DI  +IE    ++ L   R  + +  Q++R+  LY+A  +  LL S +  S  N  L   + + ++  +T + + Y + +F  L  D+RS   +   + ++V  L R
Sbjct:  188 AVESGNLFHGDKVFFKLLSNSARKHTKEVFESYLKRCQRDITVEIEKHYCDTNLSEARQNMSVIAQVIRTAPLYYAQTLQRLLPSQEVHSI-NRALYIIVWSHHKGILTSVMENYESTHFTQLMMDVRSQCKNAEARQLMVNILQR 332          
BLAST of SMED30014090 vs. Planmine SMEST
Match: SMESG000012851.1 (SMESG000012851.1)

HSP 1 Score: 847.81 bits (2189), Expect = 0.000e+0
Identity = 416/416 (100.00%), Postives = 416/416 (100.00%), Query Frame = 3
Query:   54 MGCKLSTQQQIVKRKISHVITGNELENGSSQFSKTFVPNDASQMLHDAIEKRNEESVVKILFMYKDEDYKLLLECFLEEYCIDPVTLAFQNLSSNTSEFVRLRLTAQMKNICHFINFHLRDKTANFQNRVLGIILGYQDVDLKQVTREYFNSYGYLLSNHIYCGFEGEILDFLSDHLNRNTEPAVFEENFTQEKNLSESFLSSPLHQIINKKRDSNTLSSSSIRKKLERKKILNNCNLNEFSRKPEFIFDDTGITNQSIQDCVKLLHDSIISHDLTDGNLIIFKLLAFYDRQTLRDIFEVYVQKYKKDIVPDIENSAPESYLRDLLVLSVQILRSDSLYFANEIHNLLKSTDEDSAKNYYLMFYLMTRNEESITQIKKVYRNHYFESLSDDIRSMVTDPLLQNILVKALARVSSKS 1301
            MGCKLSTQQQIVKRKISHVITGNELENGSSQFSKTFVPNDASQMLHDAIEKRNEESVVKILFMYKDEDYKLLLECFLEEYCIDPVTLAFQNLSSNTSEFVRLRLTAQMKNICHFINFHLRDKTANFQNRVLGIILGYQDVDLKQVTREYFNSYGYLLSNHIYCGFEGEILDFLSDHLNRNTEPAVFEENFTQEKNLSESFLSSPLHQIINKKRDSNTLSSSSIRKKLERKKILNNCNLNEFSRKPEFIFDDTGITNQSIQDCVKLLHDSIISHDLTDGNLIIFKLLAFYDRQTLRDIFEVYVQKYKKDIVPDIENSAPESYLRDLLVLSVQILRSDSLYFANEIHNLLKSTDEDSAKNYYLMFYLMTRNEESITQIKKVYRNHYFESLSDDIRSMVTDPLLQNILVKALARVSSKS
Sbjct:    1 MGCKLSTQQQIVKRKISHVITGNELENGSSQFSKTFVPNDASQMLHDAIEKRNEESVVKILFMYKDEDYKLLLECFLEEYCIDPVTLAFQNLSSNTSEFVRLRLTAQMKNICHFINFHLRDKTANFQNRVLGIILGYQDVDLKQVTREYFNSYGYLLSNHIYCGFEGEILDFLSDHLNRNTEPAVFEENFTQEKNLSESFLSSPLHQIINKKRDSNTLSSSSIRKKLERKKILNNCNLNEFSRKPEFIFDDTGITNQSIQDCVKLLHDSIISHDLTDGNLIIFKLLAFYDRQTLRDIFEVYVQKYKKDIVPDIENSAPESYLRDLLVLSVQILRSDSLYFANEIHNLLKSTDEDSAKNYYLMFYLMTRNEESITQIKKVYRNHYFESLSDDIRSMVTDPLLQNILVKALARVSSKS 416          
The following BLAST results are available for this feature:
BLAST of SMED30014090 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 SMED30014090 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 SMED30014090 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 SMED30014090 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 SMED30014090 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 SMED30014090 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 SMED30014090 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 SMED30014090 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
R7UAT15.878e-927.86Uncharacterized protein OS=Capitella teleta OX=283... [more]
A0A1S3IH549.188e-626.03uncharacterized protein LOC106164243 OS=Lingula un... [more]
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BLAST of SMED30014090 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 SMED30014090 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 SMED30014090 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 SMED30014090 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 SMED30014090 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 SMED30014090 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000012851.10.000e+0100.00SMESG000012851.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014090 ID=SMED30014090|Name=SMED30014090|organism=Schmidtea mediterranea sexual|type=transcript|length=1425bp
ATTTCTTTTAGTTTTCATTCTCAATGTTCGAATCCTGTTGATCTATTGTA
ATAATGGGTTGCAAGTTATCGACTCAACAGCAAATTGTGAAACGAAAAAT
TAGCCATGTTATCACCGGGAATGAACTGGAAAACGGCAGCAGCCAATTTT
CCAAAACATTTGTCCCAAATGACGCTTCACAGATGTTACATGATGCAATT
GAAAAAAGAAATGAAGAGTCAGTAGTAAAGATTCTATTTATGTACAAAGA
TGAAGACTACAAGTTGTTGTTAGAGTGTTTCCTAGAGGAATACTGTATAG
ACCCAGTCACGTTAGCATTTCAAAATCTCTCCAGTAACACTTCGGAATTT
GTGAGACTCAGATTGACAGCTCAAATGAAAAATATTTGTCACTTTATAAA
TTTTCATTTACGTGACAAAACTGCGAACTTCCAAAATCGAGTTTTGGGCA
TTATCCTCGGTTATCAGGATGTTGATCTGAAACAAGTGACCCGTGAATAC
TTCAACAGCTATGGCTATTTGCTTTCAAATCACATATATTGCGGTTTCGA
AGGTGAAATATTGGACTTTTTAAGTGACCATTTAAATAGAAACACTGAAC
CTGCAGTTTTTGAGGAAAATTTCACTCAAGAAAAAAATCTTTCTGAATCT
TTCCTCTCATCCCCTCTTCACCAAATTATCAACAAAAAACGCGACAGTAA
TACCTTGTCAAGTAGTTCAATTCGAAAGAAATTAGAAAGAAAAAAAATCT
TGAACAACTGTAACTTGAATGAATTTTCTAGGAAACCAGAATTTATTTTT
GACGACACCGGAATCACTAATCAAAGCATTCAAGATTGCGTTAAACTTCT
TCATGATTCGATCATTTCCCATGATCTTACTGATGGAAATTTAATTATTT
TTAAACTGTTGGCATTCTATGACCGTCAGACGTTGAGAGATATATTTGAA
GTTTACGTTCAAAAATATAAAAAAGATATAGTTCCTGACATTGAAAATTC
AGCCCCAGAAAGCTATTTGCGAGATCTACTTGTATTATCAGTACAAATTT
TAAGAAGTGATTCGCTTTACTTTGCCAATGAAATTCACAATCTTTTGAAG
TCGACCGACGAAGATTCAGCCAAAAATTATTATTTGATGTTTTATCTTAT
GACACGAAATGAAGAGTCCATTACACAAATAAAAAAGGTGTACCGAAATC
ACTATTTCGAATCCCTCAGTGATGATATCCGGTCTATGGTGACAGATCCA
TTGCTTCAAAACATCCTCGTCAAAGCTCTCGCAAGAGTTTCTTCAAAATC
TTGAAATATTTGTTTAAATGTGCTACTGGATAGCAACATTGTTAATGTTT
TATTTGTTTTAATGAATATTCATTGATGAATTTTTGTGTTGACGCAAAGC
CACAATTGATTTAAAACGAATTCTG
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protein sequence of SMED30014090-orf-1

>SMED30014090-orf-1 ID=SMED30014090-orf-1|Name=SMED30014090-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=417bp
MGCKLSTQQQIVKRKISHVITGNELENGSSQFSKTFVPNDASQMLHDAIE
KRNEESVVKILFMYKDEDYKLLLECFLEEYCIDPVTLAFQNLSSNTSEFV
RLRLTAQMKNICHFINFHLRDKTANFQNRVLGIILGYQDVDLKQVTREYF
NSYGYLLSNHIYCGFEGEILDFLSDHLNRNTEPAVFEENFTQEKNLSESF
LSSPLHQIINKKRDSNTLSSSSIRKKLERKKILNNCNLNEFSRKPEFIFD
DTGITNQSIQDCVKLLHDSIISHDLTDGNLIIFKLLAFYDRQTLRDIFEV
YVQKYKKDIVPDIENSAPESYLRDLLVLSVQILRSDSLYFANEIHNLLKS
TDEDSAKNYYLMFYLMTRNEESITQIKKVYRNHYFESLSDDIRSMVTDPL
LQNILVKALARVSSKS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR037104Annexin_sf
IPR018502Annexin_repeat
Vocabulary: molecular function
TermDefinition
GO:0005509calcium ion binding
GO:0005544calcium-dependent phospholipid binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR037104Annexin superfamilyGENE3DG3DSA:1.10.220.10coord: 337..411
e-value: 9.3E-6
score: 27.7
IPR037104Annexin superfamilySUPERFAMILYSSF47874Annexincoord: 33..399
NoneNo IPR availablePANTHERPTHR10502ANNEXINcoord: 260..395