SMED30032420

Overview
NameSMED30032420
Smed IDSMED30032420
Length (bp)1014
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 SMED30032420 (SMED30032420) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30032420 (SMED30032420) 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 SMED30032420 (SMED30032420) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30032420 (SMED30032420) 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



SMED30032420

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
pharynxSMED30032420h1SMcG0005194 dd_Smed_v4_1219_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30032420h1SMcG0005194 dd_Smed_v4_1219_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30032420h1SMcG0005194 dd_Smed_v4_1219_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30032420h1SMcG0005194 dd_Smed_v4_1219_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30032420h1SMcG0005194 dd_Smed_v4_1219_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30032420h1SMcG0005194 dd_Smed_v4_1219_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30032420h1SMcG0005194 dd_Smed_v4_1219_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30032420h1SMcG0005194 dd_Smed_v4_1219_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30032420h1SMcG0005194 dd_Smed_v4_1219_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30032420h1SMcG0005194 dd_Smed_v4_1219_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30032420h1SMcG0005194 Contig45850uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30032420h1SMcG0005194 Contig45850newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30032420h1SMcG0005194 OX_Smed_1.0.13602ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
secretory systemSMED30032420h1SMcG0005195 dd_Smed_v6_1219_1dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
secretory systemSMED30032420h1SMcG0005194 dd_Smed_v6_1219_1dd_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
Homology
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BLAST of SMED30032420 vs. Planmine SMEST
Match: SMESG000050221.1 (SMESG000050221.1)

HSP 1 Score: 142.895 bits (359), Expect = 1.061e-41
Identity = 67/67 (100.00%), Postives = 67/67 (100.00%), Query Frame = -1 
Query:  100 MNKFSRIDDSTDPILQQPPEYPGISTHQTSYVGNHGQTTVIIQQPSISTGGRLWSSGICSCFDDMES 300
            MNKFSRIDDSTDPILQQPPEYPGISTHQTSYVGNHGQTTVIIQQPSISTGGRLWSSGICSCFDDMES
Sbjct:    1 MNKFSRIDDSTDPILQQPPEYPGISTHQTSYVGNHGQTTVIIQQPSISTGGRLWSSGICSCFDDMES 67
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BLAST of SMED30032420 vs. Planmine SMEST
Match: SMESG000050211.1 (SMESG000050211.1)

HSP 1 Score: 102.449 bits (254), Expect = 1.802e-34
Identity = 63/106 (59.43%), Postives = 73/106 (68.87%), Query Frame = -2 
Query:  366 PKSVTDAVNKMFVNELN----IKQIAQVTKLGK-----IKESIIILETEYNKLNKQITELINGITRVKLKM---NNQSSKTKSKQNLTDDEITSTKKTFSAIDDRM 647
            P++  DAVNK FV ELN     KQI Q+ K+G+     IK  I++LET YNK   QI +L   I R+  +M   NNQSSK KSKQNLTDDEITSTKKTFSAIDDRM
Sbjct:   54 PQNDLDAVNKKFVKELNRESNTKQIVQINKIGERLDEEIKRYIMLLETGYNK---QINKLTTSINRINFEMSEMNNQSSKVKSKQNLTDDEITSTKKTFSAIDDRM 156

HSP 2 Score: 62.7734 bits (151), Expect = 1.802e-34
Identity = 31/40 (77.50%), Postives = 33/40 (82.50%), Query Frame = -3 
Query:  686 MSIVIPVNTGGGTMALNAKEILE*VESKFVNENGDRMNGD 805
            MSIVIP N GGGT+ALN K ILE VESKFVNENGD M G+
Sbjct:    1 MSIVIPENIGGGTLALNTKAILEQVESKFVNENGDSMRGE 40
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BLAST of SMED30032420 vs. Planmine SMEST
Match: SMESG000050229.1 (SMESG000050229.1)

HSP 1 Score: 102.449 bits (254), Expect = 2.826e-26
Identity = 49/66 (74.24%), Postives = 55/66 (83.33%), Query Frame = -1 
Query:  100 NKFSRIDDSTDPILQQPPEYPGISTHQTSYVGNHGQTTVIIQQPSISTGGRLWSSGICSCFDDMES 297
            NKF+  DD+ +PILQQPP YPG+S  Q SY    GQTTVIIQQP+IS+GGRLWSSGICSCFDDMES
Sbjct:    9 NKFNSADDANEPILQQPPAYPGVSVGQPSY---PGQTTVIIQQPNISSGGRLWSSGICSCFDDMES 71
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BLAST of SMED30032420 vs. Planmine SMEST
Match: SMESG000028604.1 (SMESG000028604.1)

HSP 1 Score: 82.8037 bits (203), Expect = 6.470e-26
Identity = 54/101 (53.47%), Postives = 63/101 (62.38%), Query Frame = -2 
Query:  381 PKSVTDAVNKMFVNELN----IKQIAQVTKLGK-----IKESIIILETEYNKLNKQITELINGITRVKLKM---NNQSSKTKSKQNLTDDEITSTKKTFSA 647
            P++  DAVNK FV +LN     KQI Q+ K+GK     IK  I++LET YNK   QI EL   I R+  +M   NNQSSK KSKQNL DDEI STKK F  
Sbjct:   54 PQNDLDAVNKNFVKKLNRESYTKQIVQINKIGKRLDEEIKRYIMLLETRYNK---QINELTTSIIRINFEMCEMNNQSSKMKSKQNLMDDEIYSTKKNFEC 151

HSP 2 Score: 53.5286 bits (127), Expect = 6.470e-26
Identity = 26/40 (65.00%), Postives = 30/40 (75.00%), Query Frame = -3 
Query:  686 MSIVIPVNTGGGTMALNAKEILE*VESKFVNENGDRMNGD 805
            MSI IP N  GGT+A+NA  ILE  ES+FVN NGDRM G+
Sbjct:    1 MSIAIPENIDGGTLAINASSILEEAESQFVNGNGDRMRGE 40
[Close]
BLAST of SMED30032420 vs. Planmine SMEST
Match: SMESG000011199.1 (SMESG000011199.1)

HSP 1 Score: 100.908 bits (250), Expect = 2.126e-24
Identity = 62/109 (56.88%), Postives = 73/109 (66.97%), Query Frame = -2 
Query:  357 PKSVTDAVNKMFVNELN----IKQIAQVTKLGK-----IKESIIILETEYNKLNKQITELINGITRVKLKM---NNQSSKTKSKQNLTDDEITSTKKTFSAIDDRMKVC 647
            P++  DAVNK F  ELN     KQI ++ ++GK     IK  II+LET YNK   QI EL   I+R+  +M   NNQSSK KSKQNLTDDEI STKKT SAIDDRMK+ 
Sbjct:   12 PQNDLDAVNKRFAKELNRESNTKQIVRINEIGKRLDEEIKRYIILLETGYNK---QINELTTSISRINFEMSEMNNQSSKMKSKQNLTDDEIYSTKKTLSAIDDRMKII 117
The following BLAST results are available for this feature:
BLAST of SMED30032420 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 SMED30032420 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 SMED30032420 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 SMED30032420 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 SMED30032420 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 SMED30032420 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 SMED30032420 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 SMED30032420 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 SMED30032420 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 SMED30032420 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 SMED30032420 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 SMED30032420 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 SMED30032420 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 SMED30032420 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000050221.11.061e-41100.00SMESG000050221.1[more]
SMESG000050211.11.802e-3459.43SMESG000050211.1[more]
SMESG000050229.12.826e-2674.24SMESG000050229.1[more]
SMESG000028604.16.470e-2653.47SMESG000028604.1[more]
SMESG000011199.12.126e-2456.88SMESG000011199.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032420 ID=SMED30032420|Name=SMED30032420|organism=Schmidtea mediterranea sexual|type=transcript|length=1014bp
GAATATAACCTCCCTATATAACAATTAGGTAATAATATTGTACAACAGCC
TACAATGACAACAAAAATATTAACAACAAACGTAAAAAGATGATCTACAA
GACTCCATGTCATCAAAACAAGAACATATTCCAGAACTCCATAATCGGCC
ACCGGTGCTAATGCTAGGCTGCTGAATAATTACTGTCGTTTGTCCGTGAT
TTCCGACATATGAGGTTTGATGTGTGGAAATTCCCGGATACTCCGGGGGC
TGTTGGAGAATTGGATCAGTTGAATCATCAATTCTGCTAAATTTATTCAT
TTTCCGTTTTGCGATTTCTAAGAATTATGTTTTCACATCCTGTTTACTGA
CTATCTACAAACCTTCATTCGGTCATCAATTGCACTAAAAGTTTTTTTAG
TTGAAGTGATTTCATCATCAGTTAGGTTTTGCTTGCTTTTCGTCTTGGAT
GATTGGTTATTCATTTTAAGCTTTACTCTAGTGATACCATTAATTAATTC
AGTAATTTGTTTATTCAATTTATTATATTCTGTTTCCAAAATTATAATAG
ATTCTTTAATCTTACCAAGTTTAGTAACTTGAGCAATCTGTTTAATATTC
AATTCGTTTACAAACATTTTATTGACAGCATCAGTAACAGATTTGGGATT
TGAAAGATTTGAAATAATATTATTATTCATGTTTAATCTCCATTCATACG
ATCACCATTTTCATTAACAAATTTACTTTCAACTTATTCCAAAATTTCCT
TGGCATTTAATGCCATTGTTCCACCACCAGTATTAACAGGAATTACAATA
CTCATTTTTTTATACAAGATTTGAAATTTTTTCTTGAAATGATGTTCCCT
TTTTTAAATTATATAAAATAAAAATACGTAATTGTCACATATTCTTGTAT
TTTCTTGTTGAAATTGCCAAGTATTATAAATTTAACCTTCGGTAAAATAT
GATTCCATTTCCTTTATTGAAATAATTCCATATGAATCAAAATAAATTTT
ATATTTTTTAGAAC
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protein sequence of SMED30032420-orf-1

>SMED30032420-orf-1 ID=SMED30032420-orf-1|Name=SMED30032420-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=110bp
MNNNIISNLSNPKSVTDAVNKMFVNELNIKQIAQVTKLGKIKESIIILET
EYNKLNKQITELINGITRVKLKMNNQSSKTKSKQNLTDDEITSTKKTFSA
IDDRMKVCR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000418head
PLANA:0000429neoblast
PLANA:0000484secretory system
PLANA:0003116parenchymal cell
PLANA:0003117parapharyngeal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..20