SMED30001579

Overview
NameSMED30001579
Smed IDSMED30001579
Length (bp)1282
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 SMED30001579 (SMED30001579) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001579 (SMED30001579) 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 SMED30001579 (SMED30001579) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001579 (SMED30001579) 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




SMED30001579

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
muscle cellSMED30001579SMESG000064601.1 dd_Smed_v4_15533_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30001579SMESG000064601.1 dd_Smed_v4_15533_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30001579SMESG000064601.1 dd_Smed_v4_15533_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
SMED30001579 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000617:124311..125629 -4006
v31.016630:5658..7022 -3938
v31.037480:1374..2642 +3772
v31.019772:6598..7687 -3567
v31.000099:180528..181617 +2841
Homology
BLAST of SMED30001579 vs. TrEMBL
Match: A0A3S0ZLL7 (CCHC-type domain-containing protein OS=Elysia chlorotica OX=188477 GN=EGW08_014501 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 4.831e-8
Identity = 55/212 (25.94%), Postives = 101/212 (47.64%), Query Frame = 2
Query:  266 DDESNVKEFIKKSXXXXXXXXXXXXLVILPLVLTGNAYSMFDMLEDNLGEKMSLENVLLTLGKTLGNTPWMTVAELKKMQWKSNENLGVHLGNLRTLMELNGKEPYGL---LRLFFVNSLRQYLAAYV--ISSPETLLI--LLAQ---LVERTKSRSTSYGLYFT--NHACVTSNSLIKCYKCHKDGHVMSQCPQLKCHKCSNHGNYA*KCK 865
            D   +V  +++K+   A++    ++   LPL L G+A +++  L D   EK   E +   L +   ++ +    +LK  +W   E + V   ++R L   +G    GL   ++L FV      ++A +  I   + + +  +L++   L  R +S S+  G+  T  + A       +KCYKC+   H+M  CP ++C KC   G+ A +CK
Sbjct:    5 DGNGDVGAWLQKAELVAKLTGVKDIATFLPLYLEGSALALYLELSD--AEKSDEEVLKQRLLEAFSDSRFTAYCKLKVARW-DGEPVDVFANDIRKLARESGFVKEGLEEVVKLAFVTGFPDSISAELQQIQGVDNMRVSDILSRARVLASRPRSGSSIQGVVATGVDAAKDGKKERLKCYKCNGP-HLMRDCPDIQCFKCGLDGHMANRCK 212          

HSP 2 Score: 28.8758 bits (63), Expect = 4.831e-8
Identity = 10/28 (35.71%), Postives = 20/28 (71.43%), Query Frame = 1
Query:  928 RAPIIIIQVNGMSKGALLDTGCSQTMIE 1011
            + P+I + VNG    A++DTGC+ ++++
Sbjct:  241 KVPLIEVAVNGTKCQAMVDTGCTMSLVK 268          
BLAST of SMED30001579 vs. Planmine SMEST
Match: SMESG000076049.1 (SMESG000076049.1)

HSP 1 Score: 188.348 bits (477), Expect = 2.040e-53
Identity = 108/134 (80.60%), Postives = 118/134 (88.06%), Query Frame = 2
Query:  203 IENNKLSRPPKLIQLFGICSGDDESNVKEFIKKSXXXXXXXXXXXXLVILPLVLTGNAYSMFDMLEDNLGEKMSLENVLLTLGKTLGNTPWMTVAELKKMQWKSNENLGVHLGNLRTLMELNGKEPYGLLRLFF 604
            +ENNKLSRPPKLIQL GICS DDESNV+EFIKKSRRAARVF EAEVL IL LVLTGNA+ MFD+L+DNLGEKMSL+N+LLTLGKT G T W+ + ELKKMQ KSNENL V+LGNLRTLMEL GKE  GLLRLFF
Sbjct:    1 MENNKLSRPPKLIQLLGICSDDDESNVQEFIKKSRRAARVFGEAEVLAILLLVLTGNAFKMFDILKDNLGEKMSLKNMLLTLGKTFGKTHWVALIELKKMQSKSNENLDVYLGNLRTLMELTGKEQDGLLRLFF 134          

HSP 2 Score: 85.5001 bits (210), Expect = 1.315e-17
Identity = 41/50 (82.00%), Postives = 43/50 (86.00%), Query Frame = 1
Query:  868 HFGKLYGRSVSATGFGQGNVRAPIIIIQVNGMSKGALLDTGCSQTMIEKY 1017
            HFGK YGRSV  TGFGQGNV APII+IQV G+SK ALLDTGCSQTMIE Y
Sbjct:  135 HFGKRYGRSVYETGFGQGNVCAPIILIQVYGISKPALLDTGCSQTMIEGY 184          
BLAST of SMED30001579 vs. Planmine SMEST
Match: SMESG000064600.1 (SMESG000064600.1)

HSP 1 Score: 176.792 bits (447), Expect = 3.775e-51
Identity = 97/106 (91.51%), Postives = 101/106 (95.28%), Query Frame = 2
Query:  203 IENNKLSRPPKLIQLFGICSGDDESNVKEFIKKSXXXXXXXXXXXXLVILPLVLTGNAYSMFDMLEDNLGEKMSLENVLLTLGKTLGNTPWMTVAELKKMQWKSNE 520
            +ENNKLSRPPKLIQ+ GICS DDESNV EFIKKSRRAARVF +AEVLVILPLVL GNAYSMFDMLEDNLGEKMSLENVLLTLGKTLGNTPWMTVAELKKMQWKSN+
Sbjct:    1 MENNKLSRPPKLIQILGICSRDDESNVNEFIKKSRRAARVFGKAEVLVILPLVLIGNAYSMFDMLEDNLGEKMSLENVLLTLGKTLGNTPWMTVAELKKMQWKSNK 106          
BLAST of SMED30001579 vs. Planmine SMEST
Match: SMESG000064797.1 (SMESG000064797.1)

HSP 1 Score: 92.4337 bits (228), Expect = 2.348e-25
Identity = 46/62 (74.19%), Postives = 52/62 (83.87%), Query Frame = 3
Query: 1107 EVLLGMDTISILRGVIVRQTKVELENKHMRPEICCF----DSNERGIIESRKVPNSVKNIED 1280
            EVLL MD  SILRGVIVR TKVEL N+HMRPEICC     D+N+RG+IES++VPNSVKNIED
Sbjct:   67 EVLLEMDATSILRGVIVRGTKVELANEHMRPEICCLSINVDTNKRGVIESKRVPNSVKNIED 128          

HSP 2 Score: 33.4982 bits (75), Expect = 2.348e-25
Identity = 15/19 (78.95%), Postives = 16/19 (84.21%), Query Frame = 1
Query:  961 MSKGALLDTGCSQTMIEKY 1017
            MSK ALL TGCSQTM+E Y
Sbjct:    1 MSKQALLYTGCSQTMVEGY 19          

HSP 3 Score: 28.8758 bits (63), Expect = 2.348e-25
Identity = 12/18 (66.67%), Postives = 13/18 (72.22%), Query Frame = 2
Query: 1016 IKRNVLLFVSGKFICYDR 1069
            IKRNVLL   GK  CY+R
Sbjct:   24 IKRNVLLVGGGKLTCYER 41          
The following BLAST results are available for this feature:
BLAST of SMED30001579 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 SMED30001579 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 SMED30001579 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 SMED30001579 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 SMED30001579 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 SMED30001579 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 SMED30001579 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 SMED30001579 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A3S0ZLL74.831e-825.94CCHC-type domain-containing protein OS=Elysia chlo... [more]
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BLAST of SMED30001579 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 SMED30001579 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 SMED30001579 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 SMED30001579 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 SMED30001579 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 SMED30001579 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000076049.12.040e-5380.60SMESG000076049.1[more]
SMESG000064600.13.775e-5191.51SMESG000064600.1[more]
SMESG000064797.12.348e-2574.19SMESG000064797.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001579 ID=SMED30001579|Name=SMED30001579|organism=Schmidtea mediterranea sexual|type=transcript|length=1282bp
CAGAATTTTGCACACACAATTTATCCCTGAAATTCGAACCAATGAAATTC
ATTACAAACTTTGTGTGCAGATTTCAAATTGATTGGACGTGAACTCACAA
GACCTTTATCGATGATTTAACTGGAAACCAGTTTACTGATTTTACAAAGA
AAATGTCTATATTAAAGAATGTCTAATGCTTCAATTATATGGTTTTATTT
GTATTGAAAACAACAAGCTATCGCGGCCACCAAAGTTGATCCAGCTTTTT
GGAATTTGCAGTGGGGATGATGAATCAAATGTCAAAGAATTTATAAAGAA
AAGCAGAAGAGCGGCTAGGGTGTTTGCGGAAGCAGAAGTCTTGGTCATTC
TACCTTTGGTTTTGACAGGAAACGCATATTCAATGTTCGACATGCTTGAA
GACAATTTGGGAGAAAAGATGTCTTTAGAAAACGTTCTTTTAACATTGGG
AAAAACATTGGGTAATACGCCTTGGATGACAGTAGCCGAATTAAAGAAAA
TGCAGTGGAAATCTAACGAAAATCTGGGCGTGCACTTGGGAAATCTCAGA
ACACTGATGGAACTCAATGGAAAAGAACCATATGGCTTACTAAGACTATT
TTTTGTAAATAGTTTACGACAGTACTTAGCAGCTTATGTAATTTCCAGCC
CTGAGACTCTTTTAATCCTTTTGGCACAATTGGTAGAAAGAACAAAGTCA
CGATCAACGTCTTATGGATTGTATTTCACTAATCATGCTTGTGTCACTTC
TAATAGTCTCATCAAATGTTACAAGTGTCACAAAGATGGACATGTGATGT
CTCAATGCCCACAATTAAAATGCCATAAGTGTAGTAATCATGGTAATTAT
GCATGAAAATGTAAAGTCATTTCGGGAAACTATATGGTCGATCCGTTAGC
GCGACTGGATTTGGCCAAGGGAATGTTCGCGCTCCAATAATAATCATCCA
AGTGAATGGAATGAGTAAGGGAGCTCTTTTGGATACTGGATGCTCACAAA
CAATGATTGAAAAGTATCAAAAGAAACGTATTGCTGTTTGTAAGTGGTAA
ATTCATCTGCTATGATCGATGAACGTCATGGGTAAAGAAACTATTGTTCA
GGTATAGAAGTTCTGCTAGGAATGGATACGATATCTATTCTAAGAGGTGT
AATTGTTCGTCAAACAAAAGTGGAGTTGGAGAATAAACACATGCGACCAG
AAATTTGTTGTTTTGATTCAAATGAGCGAGGAATCATAGAATCAAGGAAG
GTGCCAAATTCTGTTAAAAACATCGAGGACAA
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protein sequence of SMED30001579-orf-1

>SMED30001579-orf-1 ID=SMED30001579-orf-1|Name=SMED30001579-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=227bp
MLQLYGFICIENNKLSRPPKLIQLFGICSGDDESNVKEFIKKSRRAARVF
AEAEVLVILPLVLTGNAYSMFDMLEDNLGEKMSLENVLLTLGKTLGNTPW
MTVAELKKMQWKSNENLGVHLGNLRTLMELNGKEPYGLLRLFFVNSLRQY
LAAYVISSPETLLILLAQLVERTKSRSTSYGLYFTNHACVTSNSLIKCYK
CHKDGHVMSQCPQLKCHKCSNHGNYA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000101muscle cell
PLANA:0002056medial muscle cell
Vocabulary: INTERPRO
TermDefinition
IPR021109Peptidase_aspartic_dom_sf
IPR001878Znf_CCHC
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0008270zinc ion binding