SMED30028629

Overview
NameSMED30028629
Smed IDSMED30028629
Length (bp)403
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 SMED30028629 (SMED30028629) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028629 (SMED30028629) 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 SMED30028629 (SMED30028629) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028629 (SMED30028629) 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



SMED30028629

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30028629 SmedASXL_005088SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30028629 dd_Smed_v4_8133_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30028629 dd_Smed_v4_8133_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30028629 dd_Smed_v4_8133_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30028629 dd_Smed_v6_8133_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
secretory systemSMED30028629 dd_Smed_v6_8133_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30028629 Contig50167newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
cement glandSMED30028629 GDAG01066997.1SmedSxl_ww_GDAG01.fsa_ntPMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
vitelline glandSMED30028629 GDAG01066997.1SmedSxl_ww_GDAG01.fsa_ntPMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028629 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.051052:1808..2209 -1956
v31.007328:3934..4335 +1947
v31.007328:6132..6534 -1700
Homology
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BLAST of SMED30028629 vs. Planmine SMEST
Match: SMESG000005262.1 (SMESG000005262.1)

HSP 1 Score: 223.787 bits (569), Expect = 4.775e-77
Identity = 109/111 (98.20%), Postives = 109/111 (98.20%), Query Frame = 3 
Query:   12 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKKNKAKYINVMKTLSSDHVLFHGMDKKMLKIVMENIKNTQAS 344
            MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKKNKAKYINVMKTLSSDHVLFHGMDKKMLKIVMENIK  QAS
Sbjct:    1 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKKNKAKYINVMKTLSSDHVLFHGMDKKMLKIVMENIKKAQAS 111
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BLAST of SMED30028629 vs. Planmine SMEST
Match: SMESG000005261.1 (SMESG000005261.1)

HSP 1 Score: 202.216 bits (513), Expect = 1.824e-68
Identity = 97/111 (87.39%), Postives = 103/111 (92.79%), Query Frame = 3 
Query:   12 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKKNKAKYINVMKTLSSDHVLFHGMDKKMLKIVMENIKNTQAS 344
            MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIK NKA YI V+KTL+SDH LF GMDK +++ VMENIK +QAS
Sbjct:    1 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKNNKADYIKVVKTLNSDHSLFSGMDKGIVRAVMENIKKSQAS 111
[Close]
BLAST of SMED30028629 vs. Planmine SMEST
Match: SMESG000057736.1 (SMESG000057736.1)

HSP 1 Score: 65.4698 bits (158), Expect = 1.518e-14
Identity = 30/85 (35.29%), Postives = 48/85 (56.47%), Query Frame = 3 
Query:   12 MKHQINFLGVVIAIFI-SLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKKNKAKYINVMKTLS 263
            M  Q  FL +VI++ + S       GC ++F+DGD+P  PI     A++  K   P+ +YD++VC +NR+K+NK   +  M   S
Sbjct:    1 MNRQRTFLSIVISVLLFSKTRSAESGCNENFEDGDVPLYPIDRVRLALSKFKNAFPQSEYDRIVCILNRVKENKELVLKAMTMTS 85
[Close]
BLAST of SMED30028629 vs. Planmine SMEST
Match: SMESG000057760.1 (SMESG000057760.1)

HSP 1 Score: 63.929 bits (154), Expect = 6.852e-14
Identity = 35/101 (34.65%), Postives = 58/101 (57.43%), Query Frame = 3 
Query:   12 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKKNKAKYINVMKTLSSDHVLFHGMDKKMLKIV 314
            MK  + FL VVI+ F  LL      C ++F D DIPF   KD  +A+  +KK + + ++D+L+CD+N++K  KA+Y+  + +   +      +DK + K V
Sbjct:   17 MKQLVIFLLVVISEFSPLLADPDNLCKNEFSDNDIPFLTAKDVKDALRKAKKEISEPEFDQLLCDLNKVKGKKAEYLPELNSPHMNKFFAVAVDKDVKKSV 117
[Close]
BLAST of SMED30028629 vs. Planmine SMEST
Match: SMESG000048005.1 (SMESG000048005.1)

HSP 1 Score: 63.1586 bits (152), Expect = 1.212e-13
Identity = 33/107 (30.84%), Postives = 64/107 (59.81%), Query Frame = 3 
Query:   12 MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANSKKTLPKEQYDKLVCDMNRIKKNKAKYINVMKTLSSDHVLFHGMDKKMLKIVMENIKN 332
            M  ++ FL VV+ IF+ +L + + GC ++FKD +I     K     +  +KK + K++++++VCD+N++K    +++N    LS   VLF  + KK+ +I+ ++  N
Sbjct:    1 MNQRLLFLYVVVTIFLLILTESSTGCSENFKDDEIIGYTTKQIKVGLDKAKKVISKKEFNEIVCDLNKVKSMSRQFVN--GKLSPAQVLFGKIYKKIEEIIKKHFPN 105
The following BLAST results are available for this feature:
BLAST of SMED30028629 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 SMED30028629 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 SMED30028629 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 SMED30028629 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 SMED30028629 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 SMED30028629 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 SMED30028629 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 SMED30028629 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 SMED30028629 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 SMED30028629 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 SMED30028629 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 SMED30028629 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 SMED30028629 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 SMED30028629 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000005262.14.775e-7798.20SMESG000005262.1[more]
SMESG000005261.11.824e-6887.39SMESG000005261.1[more]
SMESG000057736.11.518e-1435.29SMESG000057736.1[more]
SMESG000057760.16.852e-1434.65SMESG000057760.1[more]
SMESG000048005.11.212e-1330.84SMESG000048005.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028629 ID=SMED30028629|Name=SMED30028629|organism=Schmidtea mediterranea sexual|type=transcript|length=403bp
TTTAGTTTAGCATGAAACATCAAATAAACTTTCTAGGAGTTGTCATTGCA
ATATTTATATCACTTTTGTTGCAATTCACAGAGGGATGCCCAGATGATTT
CAAGGATGGCGACATTCCCTTTACGCCAATTAAAGATTTCAATGAAGCCA
TGGCGAATTCAAAGAAAACCTTACCGAAAGAGCAGTATGATAAATTGGTA
TGCGATATGAACCGAATCAAAAAAAACAAGGCTAAATACATCAATGTGAT
GAAGACACTCAGTAGTGACCACGTGCTGTTTCATGGAATGGACAAAAAAA
TGTTGAAGATAGTCATGGAAAATATTAAGAACACACAAGCCTCGTAACTG
CTAAACCCGTTTAATAAATTTTTGGATTATTGTTATTGATTTTGTTTATC
AGC
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protein sequence of SMED30028629-orf-1

>SMED30028629-orf-1 ID=SMED30028629-orf-1|Name=SMED30028629-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=112bp
MKHQINFLGVVIAIFISLLLQFTEGCPDDFKDGDIPFTPIKDFNEAMANS
KKTLPKEQYDKLVCDMNRIKKNKAKYINVMKTLSSDHVLFHGMDKKMLKI
VMENIKNTQAS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000224cement gland
PLANA:0000231vitelline gland
PLANA:0000418head
PLANA:0000484secretory system
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..25
score: 0.861
NoneNo IPR availableTMHMMTMhelixcoord: 5..22