SMED30015125

Overview
NameSMED30015125
Smed IDSMED30015125
Length (bp)635
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 SMED30015125 (SMED30015125) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30015125 (SMED30015125) 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 SMED30015125 (SMED30015125) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30015125 (SMED30015125) 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



SMED30015125

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



PAGE Curations: 15

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30015125h1SMcG0018434 SmedASXL_008886SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30015125h1SMcG0018434 dd_Smed_v4_12632_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30015125h1SMcG0018434 dd_Smed_v4_12632_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30015125h1SMcG0018434 dd_Smed_v4_12632_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30015125h1SMcG0018434 dd_Smed_v4_12632_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30015125h1SMcG0018434 dd_Smed_v4_12632_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30015125h1SMcG0018434 dd_Smed_v6_12632_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
oocyteSMED30015125h1SMcG0004907 Contig4435GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30015125h1SMcG0004907 Contig4435GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30015125h1SMcG0004907 Contig4435GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30015125h1SMcG0018434 Contig4435GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30015125h1SMcG0018434 Contig4435GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30015125h1SMcG0018434 Contig4435GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
epidermisSMED30015125h1SMcG0018434 dd_Smed_v4_12632_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30015125h1SMcG0018434 dd_Smed_v4_12632_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
SMED30015125 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000026:47721..51064 +3053
Homology
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BLAST of SMED30015125 vs. TrEMBL
Match: A0A0R3XAL7 (Uncharacterized protein OS=Hydatigena taeniaeformis OX=6205 GN=TTAC_LOCUS10577 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 9.033e-7
Identity = 36/98 (36.73%), Postives = 57/98 (58.16%), Query Frame = 2 
Query:   62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISG---CVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNE 346
            ML   G+P+LF LFA  ++  LIGG ++GSG + N   K ++G+I+   G   CVLF I F++  I++R+  K+     ++ Q  F  N+  Q  D+E
Sbjct:    1 MLLFEGEPILFILFALFILSFLIGGCMWGSGEEANDRTKHIVGIIIFFFGVTCCVLFFILFIYKKIRQRRREKKDFEELMRMQNEFAANEGFQ--DDE 96
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BLAST of SMED30015125 vs. TrEMBL
Match: A0A0R3SPF6 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS6841 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 1.001e-6
Identity = 35/102 (34.31%), Postives = 59/102 (57.84%), Query Frame = 2 
Query:   62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISG---CVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNEALNV 358
            ML   G+P+LF LFA  ++  LIGG ++GSG +     K ++G+I+   G   CVLF + F +  I++++  +E K  E Q   M N+  T Q++ ++  +V
Sbjct:    1 MLLFEGEPVLFILFALFILSFLIGGCMWGSGEEAQDEPKYIVGIIIFFFGVTCCVLFFVLFTYKKIRQKR--REEKEFE-QLMRMQNEFATNQAFHDDEYSV 99
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BLAST of SMED30015125 vs. TrEMBL
Match: A0A0R3UN72 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS9232 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 3.276e-6
Identity = 33/99 (33.33%), Postives = 55/99 (55.56%), Query Frame = 2 
Query:   62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISG---CVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQS--YDN 343
            ML   G+P LF LF+++++  LIGG L+GSG D     K  +G+++   G   CV F + F +  IK+++  K+     ++ Q  F  N+  Q+  YD+
Sbjct:    1 MLLFEGEPALFLLFSASILSFLIGGCLWGSGEDAGNQAKRTVGIVIFFCGVTCCVAFFMLFTYKTIKRKRREKQDFEELMRMQNEFAANEGFQNDEYDD 99
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BLAST of SMED30015125 vs. TrEMBL
Match: A0A3P6PVJ9 (Uncharacterized protein OS=Dibothriocephalus latus OX=60516 GN=DILT_LOCUS1233 PE=4 SV=1)

HSP 1 Score: 53.5286 bits (127), Expect = 5.611e-6
Identity = 34/90 (37.78%), Postives = 49/90 (54.44%), Query Frame = 2 
Query:   62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISG---CVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNK 322
            ML   G+PLLF LF  +++  LIGG ++G G D N   + V G+ +   G   CV F I FV+  IKK +  K   A  ++ Q  F +N+
Sbjct:    1 MLLFEGEPLLFTLFGLSVLSLLIGGCMWGVGTDTNDHPRYVAGISVFFFGTGCCVCFIIVFVYKHIKKMRIRKRDLAEVVRLQNEFAENE 90
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BLAST of SMED30015125 vs. Planmine SMEST
Match: SMESG000061766.1 (SMESG000061766.1)

HSP 1 Score: 201.06 bits (510), Expect = 7.249e-67
Identity = 101/103 (98.06%), Postives = 101/103 (98.06%), Query Frame = 2 
Query:   62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISGCVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNEALNVTVPL 370
            MLFCNGDPLLFG FASAMI TLIGGMLYGSGVDNNILEKTVIGLILLISGCVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNEALNVTVPL
Sbjct:    1 MLFCNGDPLLFGFFASAMISTLIGGMLYGSGVDNNILEKTVIGLILLISGCVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNEALNVTVPL 103
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BLAST of SMED30015125 vs. Planmine SMEST
Match: SMESG000061777.1 (SMESG000061777.1)

HSP 1 Score: 80.8777 bits (198), Expect = 8.229e-20
Identity = 48/98 (48.98%), Postives = 68/98 (69.39%), Query Frame = 2 
Query:   62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISGCVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNEALN 355
            ML CNGDP+LFGLFA  ++ TLIGGML+G G    I  K + GL+LL SGC L  IG   ++IKK++ +K+ K +E+++Q MF K +T   + N+AL+
Sbjct:    1 MLLCNGDPVLFGLFAFGILSTLIGGMLFGQGEYYLIKVKRIAGLVLLCSGCALLIIGIFVIVIKKQQKIKQVKNLEIERQNMFRKKETGTGFTNDALD 98
[Close]
BLAST of SMED30015125 vs. Planmine SMEST
Match: SMESG000008768.1 (SMESG000008768.1)

HSP 1 Score: 49.6766 bits (117), Expect = 3.162e-7
Identity = 38/103 (36.89%), Postives = 53/103 (51.46%), Query Frame = 2 
Query:   62 MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISGCVLFAIGFVFLIIKKRKTLKESKAIELQKQE---MFN----KNKTTQSYDNEA 349
            ML C GD LLFGL++ A+I  LIGG L+G G D N   K   G+++ I G  +  I  +  I K  K + + + I    +E   +FN    KN   Q+  N A
Sbjct:    1 MLLCGGDQLLFGLYSVAIICLLIGGCLWGQGQDKNDSAKLTAGIVVFIIGGSIAIIAVIVNIFKSLKKMNKRRKIARMSKEKPLVFNKEQLKNPNIQNIQNHA 103
The following BLAST results are available for this feature:
BLAST of SMED30015125 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 SMED30015125 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 SMED30015125 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 SMED30015125 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 SMED30015125 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 SMED30015125 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 SMED30015125 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 SMED30015125 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A0R3XAL79.033e-736.73Uncharacterized protein OS=Hydatigena taeniaeformi... [more]
A0A0R3SPF61.001e-634.31Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
A0A0R3UN723.276e-633.33Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A3P6PVJ95.611e-637.78Uncharacterized protein OS=Dibothriocephalus latus... [more]
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BLAST of SMED30015125 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 SMED30015125 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 SMED30015125 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 SMED30015125 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 SMED30015125 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 SMED30015125 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000061766.17.249e-6798.06SMESG000061766.1[more]
SMESG000061777.18.229e-2048.98SMESG000061777.1[more]
SMESG000008768.13.162e-736.89SMESG000008768.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015125 ID=SMED30015125|Name=SMED30015125|organism=Schmidtea mediterranea sexual|type=transcript|length=635bp
CTTTTTATTGATTTTTTAAAAACTATTCTTTTTAGTATTAATTTTTTTGT
CACATTGGAAAATGCTTTTTTGCAACGGTGATCCACTTTTGTTTGGACTT
TTTGCTTCAGCAATGATCTTTACTTTGATTGGCGGAATGCTCTACGGTTC
CGGCGTAGATAATAACATTTTAGAGAAAACGGTAATTGGTTTAATTCTTT
TAATTAGTGGATGCGTATTATTTGCTATCGGTTTTGTGTTTTTGATCATC
AAAAAAAGAAAGACTCTCAAAGAATCCAAGGCCATTGAACTACAAAAACA
AGAAATGTTTAATAAAAACAAAACAACTCAATCATATGACAATGAAGCTT
TGAACGTCACAGTTCCATTGTGATATCCCCGATTGAATTTATATTTTATA
ATTCATTCTTGGATCGTAAAAATGCTTGTAAAAACATCCATGACAATTCC
GAAAAAAAGATATAACGAACAAATGAGAGAAACCAATATTTTCTAATACA
CGCTTTACAGATTTTGCTTGTTATTGCAATCACAATTTATGGCTAAATTT
TTATTTCAACGCATTGACTCAAGCGCAGGAGTTTTTAGATGTAGACGTTT
TGGATATTGATATTATAATAAATGTTATTAGTGGC
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protein sequence of SMED30015125-orf-1

>SMED30015125-orf-1 ID=SMED30015125-orf-1|Name=SMED30015125-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp
MLFCNGDPLLFGLFASAMIFTLIGGMLYGSGVDNNILEKTVIGLILLISG
CVLFAIGFVFLIIKKRKTLKESKAIELQKQEMFNKNKTTQSYDNEALNVT
VPL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000018Category 4 cell
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000074oocyte
PLANA:0000099neuron
PLANA:0000231vitelline gland
PLANA:0000418head
PLANA:0002089reproductive organ
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 41..63
NoneNo IPR availableTMHMMTMhelixcoord: 9..31