SMED30007385

Overview
NameSMED30007385
Smed IDSMED30007385
Length (bp)970
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 SMED30007385 (SMED30007385) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007385 (SMED30007385) 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 SMED30007385 (SMED30007385) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007385 (SMED30007385) 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




SMED30007385

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30007385SMESG000003089.1 dd_Smed_v4_780_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30007385SMESG000003089.1 dd_Smed_v4_780_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30007385SMESG000003089.1 dd_Smed_v4_780_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30007385SMESG000003089.1 dd_Smed_v4_780_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007385SMESG000003089.1 dd_Smed_v4_780_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007385SMESG000003089.1 dd_Smed_v4_780_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30007385SMESG000003089.1 dd_Smed_v4_780_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007385SMESG000003089.1 SMESG000077686.1 Contig51278newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007385SMESG000003089.1 SMESG000077686.1 Contig51278uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
progenitor cellSMED30007385SMESG000003089.1 dd_Smed_v6_780_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pigment cellSMED30007385SMESG000003089.1 dd_Smed_v6_780_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30007385SMESG000003089.1 dd_Smed_v6_780_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
glial cellSMED30007385SMESG000003089.1 dd_Smed_v6_780_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30007385 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000085:29342..30305 -4739
Homology
BLAST of SMED30007385 vs. TrEMBL
Match: A0A1I8GYZ1 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=3 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 4.278e-6
Identity = 36/98 (36.73%), Postives = 46/98 (46.94%), Query Frame = 3
Query:  570 NCYICNSLMDPDCEVSAKLEQKFKFPCPAT---------NKGYCLTIVQQIDKLGSVLQRNCSFNTEKSLLGCTDRVGVYKLKSRYCYCEGDFCNSAN 836
            +CYICNSL+D +CEV    + K       T         N   C    Q I+ L +++ R C    E     C DRVG  K+K +YC C    CNSAN
Sbjct: 1987 SCYICNSLVDKNCEVDPSADYKVNCSVGRTVGPDRIAVPNAQVCWKQSQDIEGL-TIVDRTCGSAVENKN-NCYDRVGTKKIKIKYCSCSTQDCNSAN 2082          
BLAST of SMED30007385 vs. Planmine SMEST
Match: SMESG000003089.1 (SMESG000003089.1)

HSP 1 Score: 251.136 bits (640), Expect = 1.641e-84
Identity = 123/124 (99.19%), Postives = 124/124 (100.00%), Query Frame = 3
Query:  501 MKFNILLISVFCGLLTSSVFASENCYICNSLMDPDCEVSAKLEQKFKFPCPATNKGYCLTIVQQIDKLGSVLQRNCSFNTEKSLLGCTDRVGVYKLKSRYCYCEGDFCNSANLMTVSTLGVFCV 872
            MKFNILLISVFCGLLTSSVFASENCYICNSL+DPDCEVSAKLEQKFKFPCPATNKGYCLTIVQQIDKLGSVLQRNCSFNTEKSLLGCTDRVGVYKLKSRYCYCEGDFCNSANLMTVSTLGVFCV
Sbjct:    1 MKFNILLISVFCGLLTSSVFASENCYICNSLIDPDCEVSAKLEQKFKFPCPATNKGYCLTIVQQIDKLGSVLQRNCSFNTEKSLLGCTDRVGVYKLKSRYCYCEGDFCNSANLMTVSTLGVFCV 124          
BLAST of SMED30007385 vs. Planmine SMEST
Match: SMESG000071975.1 (SMESG000071975.1)

HSP 1 Score: 67.0106 bits (162), Expect = 1.906e-13
Identity = 43/122 (35.25%), Postives = 63/122 (51.64%), Query Frame = 3
Query:  489 RILLMKFNILLISVFCGLLTSSVFASENCYICNSLMDP-DCEVSAKLEQKFKFPCPATNKGYCLTIVQQIDKLGSVLQRNCSFNTEKSLLGCTDRVGVYKLKSRYCYCEGDFCNSANLMTVS 851
            ++ +M  N   +  FC  LT SV  +  C +CNS +D  +CE        FK  CP  +K  C  I+Q++ +   V+ R CS   E   L C  RVG  K+K  YC+C+GD+CN +    +S
Sbjct:    2 KVYMMTNNWFALVGFCFFLTISVGNAIKCIVCNSYIDAMNCEPWDNFS--FKSDCPPESKT-CTKIIQEVHEQVRVI-RQCSGAIENDDLKCYKRVGRKKVKMYYCHCDGDYCNESPSRNIS 119          
BLAST of SMED30007385 vs. Planmine SMEST
Match: SMESG000071975.1 (SMESG000071975.1)

HSP 1 Score: 65.0846 bits (157), Expect = 7.570e-13
Identity = 43/119 (36.13%), Postives = 61/119 (51.26%), Query Frame = 3
Query:  498 LMKFNILLISVFCGLLTSSVFASENCYICNSLMDP-DCEVSAKLEQKFKFPCPATNKGYCLTIVQQIDKLGSVLQRNCSFNTEKSLLGCTDRVGVYKLKSRYCYCEGDFCNSANLMTVS 851
            +M  N   +  FC  LT SV  +  C +CNS +D  +CE        FK  CP  +K  C  I+Q++ +   V+ R CS   E   L C  RVG  K+K  YC+C+GD+CN +    +S
Sbjct:    1 MMTNNWFALVGFCFFLTISVGNAIKCIVCNSYIDAMNCEPWDNFS--FKSDCPPESKT-CTKIIQEVHEQVRVI-RQCSGAIENDDLKCYKRVGRKKVKMYYCHCDGDYCNESPSRNIS 115          
BLAST of SMED30007385 vs. Planmine SMEST
Match: SMESG000071975.1 (SMESG000071975.1)

HSP 1 Score: 64.3142 bits (155), Expect = 1.452e-12
Identity = 43/118 (36.44%), Postives = 60/118 (50.85%), Query Frame = 3
Query:  501 MKFNILLISVFCGLLTSSVFASENCYICNSLMDP-DCEVSAKLEQKFKFPCPATNKGYCLTIVQQIDKLGSVLQRNCSFNTEKSLLGCTDRVGVYKLKSRYCYCEGDFCNSANLMTVS 851
            M  N   +  FC  LT SV  +  C +CNS +D  +CE        FK  CP  +K  C  I+Q++ +   V+ R CS   E   L C  RVG  K+K  YC+C+GD+CN +    +S
Sbjct:    1 MTNNWFALVGFCFFLTISVGNAIKCIVCNSYIDAMNCEPWDNFS--FKSDCPPESKT-CTKIIQEVHEQVRVI-RQCSGAIENDDLKCYKRVGRKKVKMYYCHCDGDYCNESPSRNIS 114          
The following BLAST results are available for this feature:
BLAST of SMED30007385 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 SMED30007385 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 SMED30007385 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 SMED30007385 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 SMED30007385 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 SMED30007385 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 SMED30007385 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 SMED30007385 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A1I8GYZ14.278e-636.73Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30007385 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 SMED30007385 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 SMED30007385 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 SMED30007385 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 SMED30007385 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 SMED30007385 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000003089.11.641e-8499.19SMESG000003089.1[more]
SMESG000071975.11.906e-1335.25SMESG000071975.1[more]
SMESG000071975.17.570e-1336.13SMESG000071975.1[more]
SMESG000071975.11.452e-1236.44SMESG000071975.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007385 ID=SMED30007385|Name=SMED30007385|organism=Schmidtea mediterranea sexual|type=transcript|length=970bp
ACATAACAAAGTTGGAAATAATGCATTAAAATAAATTTACTTTATTCAAA
CAAAATCATTTTAGTTATAGTAATGTCTAATCTTGCAAGCCTGTATAAAA
AATGAAAATAATAAGTTGCAAAATTGTGTTAAAAATCCGCTAATCATAAC
CAACAGTCAAATACATCATTCAAAGTTCATTTGTAGTCAGTAATATATCT
GGAATTGCAAGATAAGTGATATATAGATCCGAAAATTGGCCTTGTTTCAG
TTAGTAAGACCTTCCAATCACGGATTTAAGACTGAACTTTGAAAACGTCA
TAAAACGGAAATGAGAGTCCAGTGAAAGTTGAACCGACGAATGCGCATCA
AACGCATAAATCATTCGCGTACAAACCTGAAGAATTATCATACACACGCA
TATGTATAAACAAGCCGCATTCAGAAGATGCGTATTCTGCACATATATAC
ACTGTAATATAAATTATTATTTATTCTTGTCCAGATTCAGAATTTTGTTG
ATGAAGTTCAACATTTTGTTAATTTCAGTATTCTGTGGCCTATTGACCAG
CTCAGTTTTTGCCAGTGAAAATTGTTACATTTGCAACTCGTTGATGGATC
CAGATTGTGAGGTCAGTGCTAAACTCGAACAGAAATTCAAATTTCCCTGT
CCAGCAACGAACAAAGGTTATTGCTTGACCATCGTCCAACAAATTGACAA
ACTCGGCAGTGTTCTTCAACGCAATTGTAGTTTCAACACTGAGAAATCTT
TATTGGGTTGTACGGATCGAGTTGGGGTTTACAAATTGAAAAGCCGCTAT
TGCTATTGTGAAGGTGATTTTTGTAATTCAGCAAACCTTATGACTGTTTC
GACATTGGGAGTATTTTGTGTAATTATTAGTTTGATAAAACAAATAATTT
AGATTATTAAATTATGTAAATGTAAATTTAGTGTAGCTATAAAATATTAG
ATCTTATTCCTGTTAAAAAA
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protein sequence of SMED30007385-orf-1

>SMED30007385-orf-1 ID=SMED30007385-orf-1|Name=SMED30007385-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=167bp
MYKQAAFRRCVFCTYIHCNINYYLFLSRFRILLMKFNILLISVFCGLLTS
SVFASENCYICNSLMDPDCEVSAKLEQKFKFPCPATNKGYCLTIVQQIDK
LGSVLQRNCSFNTEKSLLGCTDRVGVYKLKSRYCYCEGDFCNSANLMTVS
TLGVFCVIISLIKQII*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000026gut
PLANA:0000120progenitor cell
PLANA:0002075pigment cell
PLANA:0003116parenchymal cell
PLANA:0007528glial cell
Vocabulary: INTERPRO
TermDefinition
IPR031424QVR
Vocabulary: biological process
TermDefinition
GO:1903818positive regulation of voltage-gated potassium channel activity
GO:0030431sleep
GO:0032222regulation of synaptic transmission, cholinergic
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR031424Protein quiverPFAMPF17064QVRcoord: 56..144
e-value: 4.6E-7
score: 30.0
NoneNo IPR availablePANTHERPTHR33562FAMILY NOT NAMEDcoord: 37..162
NoneNo IPR availableSUPERFAMILYSSF57302Snake toxin-likecoord: 57..144
NoneNo IPR availableTMHMMTMhelixcoord: 31..53
NoneNo IPR availableTMHMMTMhelixcoord: 140..162