SMED30031935

Overview
NameSMED30031935
Smed IDSMED30031935
Length (bp)1570
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 SMED30031935 (SMED30031935) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031935 (SMED30031935) 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 SMED30031935 (SMED30031935) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031935 (SMED30031935) 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



SMED30031935

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pigment cellSMED30031935SMESG000038209.1 SmedASXL_070574SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
X1 cellSMED30031935SMESG000038209.1 SmedASXL_070574SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30031935SMESG000038209.1 SmedASXL_070574SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
cephalic gangliaSMED30031935SMESG000038209.1 dd_Smed_v4_14806_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30031935SMESG000038209.1 dd_Smed_v4_14806_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30031935SMESG000038209.1 dd_Smed_v6_14806_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30031935SMESG000055799.1 SMESG000038209.1 OX_Smed_1.0.06917ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
zeta neoblastSMED30031935SMESG000038209.1 dd_Smed_v4_14806_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
SMED30031935 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006802:10878..12444 -7537
v31.014760:3522..5097 +7510
Homology
[Close]
BLAST of SMED30031935 vs. TrEMBL
Match: A0A139WAK1 (Retrovirus-related Pol polyprotein from transposon 412-like Protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031614 PE=4 SV=1)

HSP 1 Score: 65.4698 bits (158), Expect = 2.988e-12
Identity = 38/88 (43.18%), Postives = 49/88 (55.68%), Query Frame = -3 
Query:  309 THFKIEIF*SLSQKFGF*NKYTPT*HRQTNGMIERFHRFLKPSIKCFSITSDWPDTLPFVRLGWCSTIHSASGLSLEQLVFGKGTYFP 572
            T F  E+F ++S+ FG  +  T   H Q NGMIER HR LK SIKC + T DW D LP V LG  S +      S  ++V+G+    P
Sbjct:  116 TQFDSELFRNMSKLFGMCHCKTTAYHPQANGMIERLHRQLKTSIKCHN-TEDWFDCLPLVLLGIRSAVKEDIKSSAAEMVYGEPLSLP 202

HSP 2 Score: 36.965 bits (84), Expect = 2.988e-12
Identity = 17/46 (36.96%), Postives = 28/46 (60.87%), Query Frame = -2 
Query:  559 NRWPEIVPLSNITADYVAKNIISS*FARYCLSSHLITTRNNHSFQN 696
             RWPE +P+ NI+A+ VA+ ++ +  AR+ +   LITT     F +
Sbjct:   76 TRWPEAIPIKNISAETVAQAMLHTWIARFGIPE-LITTDRGTQFDS 120
[Close]
BLAST of SMED30031935 vs. TrEMBL
Match: A0A139W8U7 (Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC031725 PE=4 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 4.798e-11
Identity = 36/88 (40.91%), Postives = 49/88 (55.68%), Query Frame = -3 
Query:  309 THFKIEIF*SLSQKFGF*NKYTPT*HRQTNGMIERFHRFLKPSIKCFSITSDWPDTLPFVRLGWCSTIHSASGLSLEQLVFGKGTYFP 572
            T F  E+F ++S+ FG  +  T   H Q NGMIER H+ LK SIKC + T +W D LP V LG  S +      S  ++V+G+    P
Sbjct: 1065 TQFDSELFRNMSKLFGICHCKTTAYHPQANGMIERLHQQLKTSIKCHN-TENWFDCLPLVLLGIRSAVKENIKSSAAEMVYGEPLSLP 1151

HSP 2 Score: 35.4242 bits (80), Expect = 4.798e-11
Identity = 16/43 (37.21%), Postives = 27/43 (62.79%), Query Frame = -2 
Query:  565 RWPEIVPLSNITADYVAKNIISS*FARYCLSSHLITTRNNHSF 693
            RWPE +P+ +I+A+ VA+ ++ +  AR+ +   LITT     F
Sbjct: 1026 RWPEAIPIKDISAETVAQALLHTWIARFGIPE-LITTDRGTQF 1067
[Close]
BLAST of SMED30031935 vs. TrEMBL
Match: A0A5S6R6D7 (Uncharacterized protein OS=Trichuris muris OX=70415 PE=4 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 1.539e-10
Identity = 35/98 (35.71%), Postives = 51/98 (52.04%), Query Frame = -3 
Query:  276 HFKIEIF*SLSQKFGF*NKYTPT*HRQTNGMIERFHRFLKPSIKCFSITSDWPDTLPFVRLGWCSTIHSASGLSLEQLVFGKGTYFPKILALEAARNN 569
             F+  +F  L + FG     T   H Q+NG+IERFHR LK ++K    TS W D LP V LG  +   + +G+S  +L +G     P    L++A+  
Sbjct: 1057 QFESVLFQKLLELFGIKRNRTTAFHPQSNGLIERFHRTLKAALKAHR-TSKWTDVLPMVLLGLRTAPKATTGVSAAELTYGTVLRLPSDFFLQSAKQE 1153

HSP 2 Score: 35.039 bits (79), Expect = 1.539e-10
Identity = 15/41 (36.59%), Postives = 23/41 (56.10%), Query Frame = -2 
Query:  571 RWPEIVPLSNITADYVAKNIISS*FARYCLSSHLITTRNNH 693
            RWPE+ P+S+I+A+ VAK   +S   R+     + T R   
Sbjct: 1017 RWPEVTPISDISAETVAKAFYASWITRFGCPETVTTDRGRQ 1057
[Close]
BLAST of SMED30031935 vs. TrEMBL
Match: A0A5S6QYA9 (Uncharacterized protein OS=Trichuris muris OX=70415 PE=4 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 1.739e-10
Identity = 35/98 (35.71%), Postives = 51/98 (52.04%), Query Frame = -3 
Query:  276 HFKIEIF*SLSQKFGF*NKYTPT*HRQTNGMIERFHRFLKPSIKCFSITSDWPDTLPFVRLGWCSTIHSASGLSLEQLVFGKGTYFPKILALEAARNN 569
             F+  +F  L + FG     T   H Q+NG+IERFHR LK ++K    TS W D LP V LG  +   + +G+S  +L +G     P    L++A+  
Sbjct: 1057 QFESVLFQKLLELFGIKRNRTTAFHPQSNGLIERFHRTLKAALKAHR-TSKWTDVLPMVLLGLRTAPKATTGVSAAELTYGTVLRLPSDFFLQSAKQE 1153

HSP 2 Score: 35.039 bits (79), Expect = 1.739e-10
Identity = 15/41 (36.59%), Postives = 23/41 (56.10%), Query Frame = -2 
Query:  571 RWPEIVPLSNITADYVAKNIISS*FARYCLSSHLITTRNNH 693
            RWPE+ P+S+I+A+ VAK   +S   R+     + T R   
Sbjct: 1017 RWPEVTPISDISAETVAKAFYASWITRFGCPETVTTDRGRQ 1057
[Close]
BLAST of SMED30031935 vs. TrEMBL
Match: A0A1Y1KS72 (Integrase catalytic domain-containing protein OS=Photinus pyralis OX=7054 PE=4 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 2.484e-10
Identity = 32/90 (35.56%), Postives = 44/90 (48.89%), Query Frame = -3 
Query:  300 HFKIEIF*SLSQKFGF*NKYTPT*HRQTNGMIERFHRFLKPSIKCFSITSDWPDTLPFVRLGWCSTIHSASGLSLEQLVFGKGTYFPKIL 569
             F+  +F  +++  G  +  T   H Q NG +ER HR LK +IKC+  T  W + LP + LG  S     SG +   LVFG     P  L
Sbjct:  198 QFESTLFAEINRMLGIKHLRTTAYHPQANGKVERLHRTLKAAIKCYR-TERWVEVLPIILLGLRSAPADDSGFAPAALVFGTALRLPGEL 286

HSP 2 Score: 41.2022 bits (95), Expect = 2.484e-10
Identity = 17/40 (42.50%), Postives = 25/40 (62.50%), Query Frame = -2 
Query:  571 WPEIVPLSNITADYVAKNIISS*FARYCLSSHLITTRNNH 690
            WPE++PLS+ITA+ VA+  IS   AR+ +   + T R   
Sbjct:  159 WPEVIPLSDITAESVARKFISEWVARFGIPEKITTDRGRQ 198
[Close]
BLAST of SMED30031935 vs. Planmine SMEST
Match: SMESG000050165.1 (SMESG000050165.1)

HSP 1 Score: 50.447 bits (119), Expect = 1.001e-6
Identity = 27/87 (31.03%), Postives = 44/87 (50.57%), Query Frame = -3 
Query:  267 HRQTNGMIERFH----------RFLKPSIKCFSITSDWPDTLPFVRLGWCSTIHSASGLSLEQLVFGKGTYFPKILALEAARNNLLK 497
            HR+T     + H          R LK +++  S +  W  +L F+ LGW +T  +++G +L QL+FGK T  P    ++   N+ LK
Sbjct:   32 HRKTRNNASKLHSIPSSDEWSTRTLKTALRILSTSKRWTKSLAFILLGWRNTPSASTGSTLSQLLFGKQTSLPSSEIIDFGNNSTLK 118
The following BLAST results are available for this feature:
BLAST of SMED30031935 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 SMED30031935 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 SMED30031935 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 SMED30031935 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 SMED30031935 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 SMED30031935 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 SMED30031935 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 SMED30031935 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A139WAK12.988e-1243.18Retrovirus-related Pol polyprotein from transposon... [more]
A0A139W8U74.798e-1140.91Uncharacterized protein OS=Tribolium castaneum OX=... [more]
A0A5S6R6D71.539e-1035.71Uncharacterized protein OS=Trichuris muris OX=7041... [more]
A0A5S6QYA91.739e-1035.71Uncharacterized protein OS=Trichuris muris OX=7041... [more]
A0A1Y1KS722.484e-1035.56Integrase catalytic domain-containing protein OS=P... [more]
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BLAST of SMED30031935 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 SMED30031935 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 SMED30031935 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 SMED30031935 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 SMED30031935 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 SMED30031935 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000050165.11.001e-631.03SMESG000050165.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031935 ID=SMED30031935|Name=SMED30031935|organism=Schmidtea mediterranea sexual|type=transcript|length=1570bp
GTCCTAAGTATATAGGCAATTTGGGATAATACTCATTTTAAATCCTAATT
ATCTGTTATCGAAATTTTTTAAGATGAATCGTGTTGTCATTGTCTGGTTA
CAATGTTATTAATTTTAAAAGAAACTGTTTGATGCGGTCCTAAGTATATA
GGTTTCGTGTAATGGATATCACGGGATAGTAGCCAGACATATTTACTTTC
ATGTAGAACTGTAGAAGTATAAGATTTATTGTAGGTTGTGGAGTTGAAAG
ATAGATTTGTGTCAAATTTTAATAAATTATTCCTAGCAGCTTCTAAAGCG
AGAATCTTAGGAAAATAGGTTCCTTTTCCGAAAACTAACTGTTCAAGTGA
TAAACCGCTGGCAGAGTGTATTGTGCTGCACCATCCTAAACGAACGAAAG
GAAGGGTATCGGGCCAATCTGATGTAATTGAAAAGCATTTGATGGAAGGT
TTTAGAAATCGGTGGAAACGTTCTATCATTCCATTGGTTTGACGATGTTA
AGTGGGGGTATATTTATTTTAAAAACCGAATTTTTGGGATAATGATCAGA
AAATTTCAATTTTGAAATGAGTGATTATTACGTGTGGTTATTAAGTGGCT
GGAAAGGCAATATCGCGCAAACTAGGAGGAGATTATATTTTTGGCCACAT
AATCAGCTGTAATGTTTGAAAGTGGAACTATTTCGGGCCATCTGTTTTCC
TGTCAACCACTTTAAGCATATAAGTCTTACCTTTGGAAGATAAGTGGCAT
ACTAGATCAACGTAAAGTAATTGGCAGCTGGAATGTGAATAATTGGAGGT
GTGATAGGGTGAATAATTTTGTTCTGTTGACATTTTATGCATTGGTTCCA
CCAAATCTTTATGAAGATTTTGATGGCATCAAATGCATTTTTTAGCTCAA
AGGGAGTATAGGTTGAGGTCAACCAAGAATGGTTATGTCGTGATAAATCT
TGTCAATGAGTTTAGCATTTTCTTTGAAGTAAGTTAAATAATCTTTAGAT
AATATACAGTTGGGTGTGTGCAATTTTGGAAAATACAGGTTGGAACAATG
TCAAAAGCTGTATTGTTCGGCCTGTTACAACCTATGTAGCATTATGGAAC
AGTTTCTTAGTTTGTGACCTTTCAGTATTTTTATTATGGTTGTTGTTGCT
TTTAACAGGACTTCGTGTCTTACAGGGAGGAATCGGGTAAGTTCGTCATT
ATTTTATTTGCAATAAAATCAAGTTTATCTATTATTGTCTTGTCTGGCCC
AGCAGATAAGCTCGAATTTTCGGTGGTAAGACTGATAAAAAAATCTACGG
AGTACTGCAGTATTTAAAGATGTTCCGGGATGCAATCTTTCGAGATCGTT
TTGAGATTTCTTTAGAAATAACGAAGGACTCCAATTTCTCAGTGACTGCG
ATTGAAAATATGAGTCAATAAGTTCAATTTCGGAAAGTTTATAATTTTAA
CTTACTGCAGACGTCTGATTCCGAATCATTGAAAATATTTGCTATTTTGT
TGATTGTAAAGTGATTGCAAAGGTTTTGTAGGTAATAGAGACATTACAAT
TTGTGCTTTTGATTCGGAAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0000429neoblast
PLANA:0002075pigment cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell