SMED30007370

Overview
NameSMED30007370
Smed IDSMED30007370
Length (bp)966
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 SMED30007370 (SMED30007370) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007370 (SMED30007370) 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 SMED30007370 (SMED30007370) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007370 (SMED30007370) 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



SMED30007370

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30007370h1SMcG0014109 dd_Smed_v4_7603_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30007370h1SMcG0014109 dd_Smed_v4_7603_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30007370h1SMcG0014109 dd_Smed_v4_7603_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
SMED30007370 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002263:44261..47482 -4654
Homology
[Close]
BLAST of SMED30007370 vs. TrEMBL
Match: A0A4U5P0B1 (PH domain-containing protein OS=Steinernema carpocapsae OX=34508 GN=L596_013490 PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 9.538e-12
Identity = 38/127 (29.92%), Postives = 69/127 (54.33%), Query Frame = 3 
Query:  111 IRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRIRLNKVFKYIAVGKIC-NMVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTETSLD 488
            +R G+L  Y + FF   S W  C+++LY D T E+Y      +  + + LN++  YI VG +  N++  RP+LP++V ID ++G         + + +F FS ++++  W + I   +  + E S+D
Sbjct:    6 VRTGWLLFYKKHFFR--SKWTRCFAVLYNDSTLEWYEKENSKNPIDSVSLNELVPYICVGYLSNNIIEIRPNLPANVSIDNLVGIKANAHPAQTHVHWFLFSCKQELDDWFKDITKTIEESVEGSVD 130
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BLAST of SMED30007370 vs. TrEMBL
Match: A0A1I7YR72 (PH domain-containing protein OS=Steinernema glaseri OX=37863 PE=4 SV=1)

HSP 1 Score: 72.4034 bits (176), Expect = 2.550e-11
Identity = 39/138 (28.26%), Postives = 70/138 (50.72%), Query Frame = 3 
Query:  111 IRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRIRLNKVFKYIAVGKICNMVPS-RPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTETSLDSKLVRENMVNG 521
            +R G+L  Y + FF   S WK C+++LY D T E++      H  + + L ++  YI VG + N +   RP LP D+ I  ++G      ++ + + +F F   E++  W + I   +  + E ++D     E++V G
Sbjct:    6 VRTGWLLFYRKRFFS--SKWKKCFAVLYGDSTLEWFAKENSKHPIDSVSLRELVPYICVGPLSNNICEIRPKLPEDMSIHQLVGIKANTHESQAHVHWFLFDSPEEVDQWFKDITRTIEESVEGTVDKN---EDLVYG 138
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BLAST of SMED30007370 vs. TrEMBL
Match: V4AF60 (PH domain-containing protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_233270 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 1.012e-10
Identity = 41/117 (35.04%), Postives = 61/117 (52.14%), Query Frame = 3 
Query:  111 IRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRIRLNKVFKYIAVGKICNMVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVL 461
            I+ GYL  Y++ FF   S WK  Y +LY D T  +Y +         ++L  V K++AVG     VP+RPDLP    I  +I FP    K  +++ +   +DQ ++  WM+ I S L
Sbjct:   18 IKTGYLKRYNKGFFS--SGWKQEYLVLYQDSTLAWYEDQGSYEPKGGVKLKNVCKFLAVGAYSQNVPNRPDLPPGGRITNLIAFPLKPDKK-AQVIWILCADQNELNSWMKDITSTL 131
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BLAST of SMED30007370 vs. TrEMBL
Match: A0A4U5P0B5 (PH domain-containing protein OS=Steinernema carpocapsae OX=34508 GN=L596_013492 PE=4 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 1.396e-10
Identity = 41/131 (31.30%), Postives = 60/131 (45.80%), Query Frame = 3 
Query:   90 LSSE*MIIRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRIRLNKVFKYIAVGKICNMVP-SRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTET 479
            +  E   IR GYL  Y   FF     WK CY++L+ D TF +Y    DS   + + L  V  YI VG +C+ +P  RP++P D  +  ++G           + +F F    D+  W + I   LP   E 
Sbjct:    1 MEGERRKIRDGYLQRYKSGFFS--KKWKDCYAVLWSDSTFSWYDEKGDSSPVDSVFLKDVIPYICVGLLCDKMPVKRPEVPEDSTVHHLVGIGM--DPKAETVHWFMFGSDSDLEAWFKDITRTLPKPAEQ 127
[Close]
BLAST of SMED30007370 vs. TrEMBL
Match: R7UAM5 (PH domain-containing protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_191509 PE=4 SV=1)

HSP 1 Score: 70.8626 bits (172), Expect = 8.975e-10
Identity = 38/118 (32.20%), Postives = 58/118 (49.15%), Query Frame = 3 
Query:  111 IRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRIRLNKVFKYIAVGKICNMVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLP 464
            +R GYL  Y +    +   WK  Y ++Y D +  ++    D        L  V  Y+ VG  C  +P  P+LP++  ID MI FP    K  S++ +F   D+ ++  WM +I SVLP
Sbjct:    8 VRSGYLQKYSKGM--LGEKWKRVYVVIYKDSSIFWFKKKDDPASKGNASLKNVCNYLTVGANCRAIPYSPELPANARIDFMIAFPQEPVKK-SKVHFFLCDDEAELNDWMTSISSVLP 122
[Close]
BLAST of SMED30007370 vs. Planmine SMEST
Match: SMESG000045571.1 (SMESG000045571.1)

HSP 1 Score: 286.574 bits (732), Expect = 1.924e-97
Identity = 171/171 (100.00%), Postives = 171/171 (100.00%), Query Frame = 3 
Query:  303 MVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTETSLDSKLVRENMVNGDNKVETGTVNRHDPGYGKXXXXXXXXXXXXXXGYDPAIXXXXXXXXXXXXXVAMTMPMWAMSSAWCPPTIIHTGSPMLIDGTNTITVGNDITMPMGGD 815
            MVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTETSLDSKLVRENMVNGDNKVETGTVNRHDPGYGKNTNYYYHNNPNYHYGYDPAIGAAAGLGLGMGLGVAMTMPMWAMSSAWCPPTIIHTGSPMLIDGTNTITVGNDITMPMGGD
Sbjct:    1 MVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYFHFSDQEDMILWMRAIDSVLPHNTETSLDSKLVRENMVNGDNKVETGTVNRHDPGYGKNTNYYYHNNPNYHYGYDPAIGAAAGLGLGMGLGVAMTMPMWAMSSAWCPPTIIHTGSPMLIDGTNTITVGNDITMPMGGD 171
The following BLAST results are available for this feature:
BLAST of SMED30007370 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 SMED30007370 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 SMED30007370 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 SMED30007370 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 SMED30007370 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 SMED30007370 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 SMED30007370 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 SMED30007370 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4U5P0B19.538e-1229.92PH domain-containing protein OS=Steinernema carpoc... [more]
A0A1I7YR722.550e-1128.26PH domain-containing protein OS=Steinernema glaser... [more]
V4AF601.012e-1035.04PH domain-containing protein OS=Lottia gigantea OX... [more]
A0A4U5P0B51.396e-1031.30PH domain-containing protein OS=Steinernema carpoc... [more]
R7UAM58.975e-1032.20PH domain-containing protein OS=Capitella teleta O... [more]
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BLAST of SMED30007370 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 SMED30007370 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 SMED30007370 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 SMED30007370 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 SMED30007370 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 SMED30007370 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000045571.11.924e-97100.00SMESG000045571.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007370 ID=SMED30007370|Name=SMED30007370|organism=Schmidtea mediterranea sexual|type=transcript|length=966bp
GTGAACCTGGTTATATCTAATTCTAATTAATCAATTAATTATATAAAGAA
TATTAATAAAGTTACTTTTAATAATTCATCATTTATATTTTAAGTTCAGA
ATAAATGATTATTAGACGAGGATACTTAACTCACTATGATGAATGTTTTT
TTGAAATTTTTAGTTGCTGGAAAGCATGTTACTCGATTTTATATTATGAT
GGTACTTTTGAATTTTATACCAATGGAAAAGATTCTCATTTCACAAATCG
AATTAGACTTAATAAAGTCTTTAAATATATCGCTGTGGGAAAAATTTGCA
ATATGGTTCCAAGTCGGCCAGATCTACCAAGTGACGTTCCAATCGATTTA
ATGATTGGTTTTCCATGTGTGAATTCTAAAAATCCCAGTGAAATGGAATA
CTTCCATTTTTCTGATCAAGAAGATATGATATTGTGGATGCGCGCCATTG
ATTCAGTTCTTCCTCATAACACAGAGACATCTTTAGACAGCAAATTGGTA
CGAGAAAACATGGTAAACGGTGACAATAAAGTTGAAACTGGAACGGTCAA
CAGACACGATCCTGGTTACGGTAAAAACACTAATTATTATTACCATAATA
ATCCAAACTATCACTATGGTTATGACCCTGCCATTGGTGCAGCCGCCGGG
CTTGGTCTCGGTATGGGCTTAGGAGTCGCCATGACAATGCCGATGTGGGC
TATGAGCAGTGCCTGGTGTCCTCCTACAATTATCCATACCGGTTCTCCTA
TGCTGATTGATGGAACCAATACCATTACAGTTGGGAATGACATAACGATG
CCCATGGGCGGTGATACGGTCACCACTACTGTAACAACTACTGATTTCAA
TCCGGGATTTGATACGAATTTCGGAAATGATTTTGGAACTGGATTTGATT
TTTAAGGTTTTATAATTTCAATCTTTCTTCTTCTGATTAGTAAATTATCA
GTTGATTGCAAAAAAA
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protein sequence of SMED30007370-orf-1

>SMED30007370-orf-1 ID=SMED30007370-orf-1|Name=SMED30007370-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=267bp
MIIRRGYLTHYDECFFEIFSCWKACYSILYYDGTFEFYTNGKDSHFTNRI
RLNKVFKYIAVGKICNMVPSRPDLPSDVPIDLMIGFPCVNSKNPSEMEYF
HFSDQEDMILWMRAIDSVLPHNTETSLDSKLVRENMVNGDNKVETGTVNR
HDPGYGKNTNYYYHNNPNYHYGYDPAIGAAAGLGLGMGLGVAMTMPMWAM
SSAWCPPTIIHTGSPMLIDGTNTITVGNDITMPMGGDTVTTTVTTTDFNP
GFDTNFGNDFGTGFDF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000035Category 3 cell
PLANA:0000054dorsal region of the epidermis
Vocabulary: INTERPRO
TermDefinition
IPR039680PLEKHB1/2
IPR011993PH-like_dom_sf
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR011993PH-like domain superfamilyGENE3DG3DSA:2.30.29.30coord: 1..122
e-value: 9.2E-7
score: 30.8
NoneNo IPR availablePANTHERPTHR14309:SF10coord: 2..124
NoneNo IPR availableSUPERFAMILYSSF50729PH domain-likecoord: 3..127
IPR039680Pleckstrin homology domain-containing family B member 1/2PANTHERPTHR14309FAMILY NOT NAMEDcoord: 2..124