SMED30033897

Overview
NameSMED30033897
Smed IDSMED30033897
Length (bp)1034
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 SMED30033897 (SMED30033897) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30033897 (SMED30033897) 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 SMED30033897 (SMED30033897) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30033897 (SMED30033897) 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




SMED30033897

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30033897SMESG000058973.1 dd_Smed_v4_11589_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30033897 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004261:13453..21014 +5039
Homology
BLAST of SMED30033897 vs. Planmine SMEST
Match: SMESG000058973.1 (SMESG000058973.1)

HSP 1 Score: 494.967 bits (1273), Expect = 2.673e-178
Identity = 266/266 (100.00%), Postives = 266/266 (100.00%), Query Frame = 3
Query:  129 MLNPMSINLTFDNFXXXXXXXXXXXXXXLKLRVSSKIKMDVKDFLLKVNNTLMKEEQLVVSLLFTDFVLTNNTNVLNIRINDLTYDFVMDIPNSEEKIHLKANSNSSILDLKIIISENIKINLKTWKMKISDNILKDIMLLTNCIEVKTIQVIANEEFDVHVINDKRNYKVSTKRDTTITEFKLAVSEKIGLPVDTFYMTFNGQSIENVRHRKFSLKSGLFFKNLFRSNISITKPVVNVVGEQMVLESFEINKNAIIHVIMRTRGG 926
            MLNPMSINLTFDNFTYSETVTTTMTVSELKLRVSSKIKMDVKDFLLKVNNTLMKEEQLVVSLLFTDFVLTNNTNVLNIRINDLTYDFVMDIPNSEEKIHLKANSNSSILDLKIIISENIKINLKTWKMKISDNILKDIMLLTNCIEVKTIQVIANEEFDVHVINDKRNYKVSTKRDTTITEFKLAVSEKIGLPVDTFYMTFNGQSIENVRHRKFSLKSGLFFKNLFRSNISITKPVVNVVGEQMVLESFEINKNAIIHVIMRTRGG
Sbjct:    1 MLNPMSINLTFDNFTYSETVTTTMTVSELKLRVSSKIKMDVKDFLLKVNNTLMKEEQLVVSLLFTDFVLTNNTNVLNIRINDLTYDFVMDIPNSEEKIHLKANSNSSILDLKIIISENIKINLKTWKMKISDNILKDIMLLTNCIEVKTIQVIANEEFDVHVINDKRNYKVSTKRDTTITEFKLAVSEKIGLPVDTFYMTFNGQSIENVRHRKFSLKSGLFFKNLFRSNISITKPVVNVVGEQMVLESFEINKNAIIHVIMRTRGG 266          
BLAST of SMED30033897 vs. Planmine SMEST
Match: SMESG000058973.1 (SMESG000058973.1)

HSP 1 Score: 486.493 bits (1251), Expect = 5.346e-175
Identity = 262/262 (100.00%), Postives = 262/262 (100.00%), Query Frame = 3
Query:  141 MSINLTFDNFXXXXXXXXXXXXXXLKLRVSSKIKMDVKDFLLKVNNTLMKEEQLVVSLLFTDFVLTNNTNVLNIRINDLTYDFVMDIPNSEEKIHLKANSNSSILDLKIIISENIKINLKTWKMKISDNILKDIMLLTNCIEVKTIQVIANEEFDVHVINDKRNYKVSTKRDTTITEFKLAVSEKIGLPVDTFYMTFNGQSIENVRHRKFSLKSGLFFKNLFRSNISITKPVVNVVGEQMVLESFEINKNAIIHVIMRTRGG 926
            MSINLTFDNFTYSETVTTTMTVSELKLRVSSKIKMDVKDFLLKVNNTLMKEEQLVVSLLFTDFVLTNNTNVLNIRINDLTYDFVMDIPNSEEKIHLKANSNSSILDLKIIISENIKINLKTWKMKISDNILKDIMLLTNCIEVKTIQVIANEEFDVHVINDKRNYKVSTKRDTTITEFKLAVSEKIGLPVDTFYMTFNGQSIENVRHRKFSLKSGLFFKNLFRSNISITKPVVNVVGEQMVLESFEINKNAIIHVIMRTRGG
Sbjct:    1 MSINLTFDNFTYSETVTTTMTVSELKLRVSSKIKMDVKDFLLKVNNTLMKEEQLVVSLLFTDFVLTNNTNVLNIRINDLTYDFVMDIPNSEEKIHLKANSNSSILDLKIIISENIKINLKTWKMKISDNILKDIMLLTNCIEVKTIQVIANEEFDVHVINDKRNYKVSTKRDTTITEFKLAVSEKIGLPVDTFYMTFNGQSIENVRHRKFSLKSGLFFKNLFRSNISITKPVVNVVGEQMVLESFEINKNAIIHVIMRTRGG 262          
BLAST of SMED30033897 vs. Planmine SMEST
Match: SMESG000058958.1 (SMESG000058958.1)

HSP 1 Score: 77.7962 bits (190), Expect = 1.507e-16
Identity = 57/172 (33.14%), Postives = 94/172 (54.65%), Query Frame = 3
Query:  243 MDVKDFLLKVNNTLMKEEQLVVSLLFTDFVLTNNTNVLNIRINDLTYDFVMDIPNSEEKIHLKANSNSSILDLKIIISENIKINLKTWKMKISDNILKDIMLLTNCIEVKTIQVIANEEFDVHVINDKRNYKVSTKRDTTITEFKLAVSEKIGLPVDTFYMTFNGQSIENVR 758
            +++ DF LK++  L+ E++ V   L T+F LT+N   + + INDLT  F + I     +I L+A +  SI DLK  I   +K+    W MK ++ I+ D   L N I+ K +  I  + F V V    R++ V+  +D TI EF+    +KIG  ++   + F+G+S++  R
Sbjct:   16 LNIADFALKIDQLLLLEDKPVHKYLNTEFSLTDNQKYIKLEINDLT--FAIKITEKSREISLEATAEISIGDLKNKIMNKLKLTGAQWSMKKNNEIIDDKDSLLNHID-KKMFTIYFQPFIVIVKCAGRSHSVTVTKDMTILEFRKECFKKIGEQINDLLVLFDGESLDYER 184          
BLAST of SMED30033897 vs. Planmine SMEST
Match: SMESG000058958.1 (SMESG000058958.1)

HSP 1 Score: 77.7962 bits (190), Expect = 2.429e-16
Identity = 57/172 (33.14%), Postives = 94/172 (54.65%), Query Frame = 3
Query:  243 MDVKDFLLKVNNTLMKEEQLVVSLLFTDFVLTNNTNVLNIRINDLTYDFVMDIPNSEEKIHLKANSNSSILDLKIIISENIKINLKTWKMKISDNILKDIMLLTNCIEVKTIQVIANEEFDVHVINDKRNYKVSTKRDTTITEFKLAVSEKIGLPVDTFYMTFNGQSIENVR 758
            +++ DF LK++  L+ E++ V   L T+F LT+N   + + INDLT  F + I     +I L+A +  SI DLK  I   +K+    W MK ++ I+ D   L N I+ K +  I  + F V V    R++ V+  +D TI EF+    +KIG  ++   + F+G+S++  R
Sbjct:   35 LNIADFALKIDQLLLLEDKPVHKYLNTEFSLTDNQKYIKLEINDLT--FAIKITEKSREISLEATAEISIGDLKNKIMNKLKLTGAQWSMKKNNEIIDDKDSLLNHID-KKMFTIYFQPFIVIVKCAGRSHSVTVTKDMTILEFRKECFKKIGEQINDLLVLFDGESLDYER 203          
BLAST of SMED30033897 vs. Planmine SMEST
Match: SMESG000058954.1 (SMESG000058954.1)

HSP 1 Score: 63.929 bits (154), Expect = 9.980e-12
Identity = 56/185 (30.27%), Postives = 91/185 (49.19%), Query Frame = 3
Query:  372 DLTYDFVMDIPNSEEKIHLKANSNSSILDLKIIISENIKINLKTWKMKISDNILKDIMLLTNCIEVKTIQVIANEEFDVHVINDKRNYKVSTKRDTTITEFKLAVSEKIGLPVDTFYMTFNGQSIENVRHRKFSLKSGLFFKNLFRSNISITKPVVNVVGEQMVLESFEINKNAIIHVIMRTRGG 926
            DLT  F + I     +I L+A +  SI DLK  I   +K+    W MK ++ I+ D   L N I+ K    I  + F V V    RNY V+  +D TI EF+    +KIG  ++ F + FNG+S++   + K      LF   LF  ++        V  + + L  +E+  N+++ ++ + +GG
Sbjct:   23 DLT--FAIKITEKSREISLEATAEISIGDLKNKIMNKLKLTGAQWSMKKNNEIIDDKDSLLNHIDKKRF-TIYFQTFVVIVNCVDRNYSVTVTKDMTILEFRKECFKKIGEQINEFLILFNGESLD---YEKVITLEDLFVGILFNIDVINIHQTEKVKKDNLTLGFYEVVPNSVLVLVPKVKGG 201          
The following BLAST results are available for this feature:
BLAST of SMED30033897 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 SMED30033897 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 SMED30033897 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 SMED30033897 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 SMED30033897 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 SMED30033897 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 SMED30033897 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 SMED30033897 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 SMED30033897 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 SMED30033897 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 SMED30033897 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 SMED30033897 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 SMED30033897 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 SMED30033897 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000058973.12.673e-178100.00SMESG000058973.1[more]
SMESG000058973.15.346e-175100.00SMESG000058973.1[more]
SMESG000058958.11.507e-1633.14SMESG000058958.1[more]
SMESG000058958.12.429e-1633.14SMESG000058958.1[more]
SMESG000058954.19.980e-1230.27SMESG000058954.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033897 ID=SMED30033897|Name=SMED30033897|organism=Schmidtea mediterranea sexual|type=transcript|length=1034bp
TAACTTTCGCTGAAATCTGATTTGTTAAACTTGGATATGCTTAATATCAT
CATTATAATCATCATCCTGATACTATAAATAGTTTATGTTTGATTTCAAT
TCCAATTATTTTAGAAATCAAGAATCGAATGCTCAATCCTATGTCAATAA
ATTTAACGTTTGACAATTTCACATATTCAGAAACCGTAACGACAACTATG
ACTGTCAGTGAATTGAAATTAAGAGTCAGTAGCAAAATCAAAATGGATGT
TAAAGATTTTCTATTAAAAGTCAACAATACCTTGATGAAGGAGGAACAGT
TAGTGGTATCACTCTTGTTCACCGATTTCGTTTTAACAAATAATACAAAC
GTTTTGAACATACGAATTAATGATTTAACTTATGATTTTGTCATGGACAT
ACCAAATTCAGAGGAAAAAATTCATTTGAAAGCCAATTCAAATAGTAGCA
TTTTAGACTTGAAAATTATAATTTCCGAAAATATAAAAATAAATTTGAAA
ACATGGAAAATGAAAATTTCTGATAATATTTTAAAGGACATAATGCTTTT
GACAAATTGTATAGAAGTTAAAACAATACAAGTGATTGCAAATGAAGAAT
TCGATGTCCATGTAATAAATGATAAAAGGAACTACAAAGTAAGCACCAAA
CGCGATACGACAATCACAGAGTTCAAGTTAGCAGTCTCAGAAAAGATCGG
TTTACCGGTTGACACATTTTACATGACTTTCAATGGACAAAGTATAGAGA
ACGTCAGGCACCGGAAATTTAGTTTGAAAAGTGGATTGTTTTTCAAAAAT
CTCTTTAGAAGCAATATTTCCATAACGAAGCCGGTAGTTAATGTTGTTGG
AGAACAGATGGTTCTTGAATCGTTTGAGATAAACAAAAATGCAATCATTC
ATGTGATAATGAGAACCAGGGGCGGTTGAAAGCAGATCTTCCAATCAAGT
CGCTGTACAAACAAATCTTTTTCAATCATCAATATCTTTGTATTATTAGC
ATTTTTTGAAATTTTAAATTTTAAGATCGGAAGA
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protein sequence of SMED30033897-orf-1

>SMED30033897-orf-1 ID=SMED30033897-orf-1|Name=SMED30033897-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=267bp
MLNPMSINLTFDNFTYSETVTTTMTVSELKLRVSSKIKMDVKDFLLKVNN
TLMKEEQLVVSLLFTDFVLTNNTNVLNIRINDLTYDFVMDIPNSEEKIHL
KANSNSSILDLKIIISENIKINLKTWKMKISDNILKDIMLLTNCIEVKTI
QVIANEEFDVHVINDKRNYKVSTKRDTTITEFKLAVSEKIGLPVDTFYMT
FNGQSIENVRHRKFSLKSGLFFKNLFRSNISITKPVVNVVGEQMVLESFE
INKNAIIHVIMRTRGG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR000626Ubiquitin-like_dom
IPR029071Ubiquitin-like_domsf
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000626Ubiquitin-like domainPROSITEPS50053UBIQUITIN_2coord: 156..208
score: 9.265
NoneNo IPR availableCDDcd17039Ubl_ubiquitin_likecoord: 160..208
e-value: 0.0065521
score: 32.5682
IPR029071Ubiquitin-like domain superfamilySUPERFAMILYSSF54236Ubiquitin-likecoord: 94..143
IPR029071Ubiquitin-like domain superfamilySUPERFAMILYSSF54236Ubiquitin-likecoord: 154..219
IPR029071Ubiquitin-like domain superfamilySUPERFAMILYSSF54236Ubiquitin-likecoord: 7..59