SMED30032290

Overview
NameSMED30032290
Smed IDSMED30032290
Length (bp)573
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 SMED30032290 (SMED30032290) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30032290 (SMED30032290) 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 SMED30032290 (SMED30032290) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30032290 (SMED30032290) 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




SMED30032290

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30032290SMESG000014241.1 SMESG000014240.1 SmedASXL_007078SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30032290SMESG000014241.1 SMESG000014240.1 SmedASXL_007079SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pigment cellSMED30032290SMESG000014241.1 SMESG000014240.1 SmedASXL_007079SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017
whole organism asexual adult RNA-sequencing evidence
gutSMED30032290SMESG000014241.1 SMESG000014240.1 dd_Smed_v4_185_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30032290SMESG000014241.1 SMESG000014240.1 dd_Smed_v6_185_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30032290SMESG000062740.1 SMESG000036199.1 SMESG000014241.1 OX_Smed_1.0.12877ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
head regionSMED30032290SMESG000014241.1 SMESG000014240.1 SMESG000054799.1 OX_Smed_1.0.16331ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
body wall musculatureSMED30032290SMESG000014241.1 SMESG000014240.1 dd_Smed_v4_185_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
goblet cellSMED30032290SMESG000014241.1 SMESG000014240.1 dd_Smed_v6_185_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30032290SMESG000074081.1 Contig1293GPL15192PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30032290SMESG000014241.1 SMESG000014240.1 Contig1293GPL15192PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Category 2 cellSMED30032290SMESG000014241.1 SMESG000014240.1 dd_Smed_v4_185_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
SMED30032290 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005875:43153..44662 +2640
v31.025677:1502..3332 -2512
Homology
BLAST of SMED30032290 vs. Planmine SMEST
Match: SMESG000014241.1 (SMESG000014241.1)

HSP 1 Score: 244.202 bits (622), Expect = 8.985e-84
Identity = 121/121 (100.00%), Postives = 121/121 (100.00%), Query Frame = 2
Query:  158 KRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELV 520
            KRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELV
Sbjct:    9 KRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELV 129          

HSP 2 Score: 48.521 bits (114), Expect = 2.168e-7
Identity = 29/63 (46.03%), Postives = 36/63 (57.14%), Query Frame = 2
Query:  143 EISKDKRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHI 331
            EISK KRS  S EY DLR+RIL     G      F+++Q F  +L  LN +EK +I   VS I
Sbjct:   70 EISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELVSQI 132          
BLAST of SMED30032290 vs. Planmine SMEST
Match: SMESG000014240.1 (SMESG000014240.1)

HSP 1 Score: 233.417 bits (594), Expect = 3.838e-78
Identity = 122/151 (80.79%), Postives = 132/151 (87.42%), Query Frame = 2
Query:   68 VCQLNSLQYSEDSNKNCDKIWKIIKEISKDKRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELV 520
            +CQLNSLQYSEDSNKNCDKIWKIIKEISKDKRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTAL SDEK KI NF+  IFDVE SK KRSS+SREYLDLRSRIL  HAKG+ +L  F++S GF  V++GLN  EK EI EL+
Sbjct:   12 ICQLNSLQYSEDSNKNCDKIWKIIKEISKDKRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNHAKGNQFLLPFITSDGFFEVMKGLNNQEKSEIYELI 162          

HSP 2 Score: 69.3218 bits (168), Expect = 1.622e-14
Identity = 40/114 (35.09%), Postives = 68/114 (59.65%), Query Frame = 2
Query:  179 EYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELV 520
            EY DLR+RIL +   G    + F+ +  F E++  LN+ EK++I   ++ I     +K  RS YS+++LDLR  IL+   KG+  L  F+     +++++ LN++E+ EI EL+
Sbjct:  115 EYLDLRSRILGNHAKGNQFLLPFITSDGFFEVMKGLNNQEKSEIYELINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGN--LGLFIRRPVTVDLIKNLNKSEQKEIYELI 226          
BLAST of SMED30032290 vs. Planmine SMEST
Match: SMESG000014240.1 (SMESG000014240.1)

HSP 1 Score: 233.802 bits (595), Expect = 4.849e-78
Identity = 122/151 (80.79%), Postives = 132/151 (87.42%), Query Frame = 2
Query:   68 VCQLNSLQYSEDSNKNCDKIWKIIKEISKDKRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELV 520
            +CQLNSLQYSEDSNKNCDKIWKIIKEISKDKRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTAL SDEK KI NF+  IFDVE SK KRSS+SREYLDLRSRIL  HAKG+ +L  F++S GF  V++GLN  EK EI EL+
Sbjct:   12 ICQLNSLQYSEDSNKNCDKIWKIIKEISKDKRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNHAKGNQFLLPFITSDGFFEVMKGLNNQEKSEIYELI 162          

HSP 2 Score: 69.3218 bits (168), Expect = 2.485e-14
Identity = 40/114 (35.09%), Postives = 68/114 (59.65%), Query Frame = 2
Query:  179 EYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELV 520
            EY DLR+RIL +   G    + F+ +  F E++  LN+ EK++I   ++ I     +K  RS YS+++LDLR  IL+   KG+  L  F+     +++++ LN++E+ EI EL+
Sbjct:  115 EYLDLRSRILGNHAKGNQFLLPFITSDGFFEVMKGLNNQEKSEIYELINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGN--LGLFIRRPVTVDLIKNLNKSEQKEIYELI 226          
BLAST of SMED30032290 vs. Planmine SMEST
Match: SMESG000014241.1 (SMESG000014241.1)

HSP 1 Score: 221.861 bits (564), Expect = 4.058e-75
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = 2
Query:  191 LRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELV 520
            LRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELV
Sbjct:    9 LRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELV 118          

HSP 2 Score: 48.521 bits (114), Expect = 1.560e-7
Identity = 29/63 (46.03%), Postives = 36/63 (57.14%), Query Frame = 2
Query:  143 EISKDKRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHI 331
            EISK KRS  S EY DLR+RIL     G      F+++Q F  +L  LN +EK +I   VS I
Sbjct:   59 EISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELVSQI 121          
BLAST of SMED30032290 vs. Planmine SMEST
Match: SMESG000014240.1 (SMESG000014240.1)

HSP 1 Score: 88.1965 bits (217), Expect = 7.839e-22
Identity = 64/162 (39.51%), Postives = 95/162 (58.64%), Query Frame = 2
Query:   68 VCQLNSLQYSEDSNKNC------DKIWKIIKEI-----SKDKRSECSDEYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELV 520
            +CQLNSLQYSEDSNKN        KI   + +I     SK KRS  S EY DLR+RIL +   G    + F+ +  F E++  LN+ EK++I   ++ I     +K  RS YS+++LDLR  IL+   KG+  L  F+     +++++ LN++E+ EI EL+
Sbjct:   12 ICQLNSLQYSEDSNKNSLKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNHAKGNQFLLPFITSDGFFEVMKGLNNQEKSEIYELINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGN--LGLFIRRPVTVDLIKNLNKSEQKEIYELI 171          
The following BLAST results are available for this feature:
BLAST of SMED30032290 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 SMED30032290 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 SMED30032290 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 SMED30032290 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 SMED30032290 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 SMED30032290 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 SMED30032290 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 SMED30032290 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 SMED30032290 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 SMED30032290 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 SMED30032290 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 SMED30032290 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 SMED30032290 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 SMED30032290 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000014241.18.985e-84100.00SMESG000014241.1[more]
SMESG000014240.13.838e-7880.79SMESG000014240.1[more]
SMESG000014240.14.849e-7880.79SMESG000014240.1[more]
SMESG000014241.14.058e-75100.00SMESG000014241.1[more]
SMESG000014240.17.839e-2239.51SMESG000014240.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032290 ID=SMED30032290|Name=SMED30032290|organism=Schmidtea mediterranea sexual|type=transcript|length=573bp
GATCGTTTGTCTTTTGAAATTTCATTAATAAATAATGTTTAAAATTTTTA
TTTTCATTTGCTTTTTTGTCTGTCAACTGAATTCTTTGCAGTATTCTGAG
GATTCCAATAAAAATTGTGATAAAATATGGAAGATTATCAAAGAAATTTC
AAAAGACAAACGATCGGAATGTTCTGATGAATATACAGATCTAAGAAACC
GCATATTAGAAAGTCGTGTTGGAGGATATCCGAGTTTTGTAACTTTTGTA
AATACTCAAGAATTTCGTGAATTATTAACCGCTTTGAATAGCGATGAAAA
GACGAAAATCGGAAATTTTGTATCACATATATTTGATGTAGAAATATCTA
AAGTAAAACGATCTTCATATTCAAGAGAGTATTTGGATTTGAGAAGTCGC
ATACTAGCTCAACATGCAAAAGGAGATTCATATTTATCAAAGTTTTTATC
CAGTCAAGGGTTCATCAACGTGTTAGAAGGTTTGAACGAAAATGAAAAAG
ACGAAATTGAAGAATTAGTTTCGCAGATAATTCAATGAACAAGCTGAATT
TTAATTAATAAATTTCATTTTGC
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protein sequence of SMED30032290-orf-1

>SMED30032290-orf-1 ID=SMED30032290-orf-1|Name=SMED30032290-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=168bp
MFKIFIFICFFVCQLNSLQYSEDSNKNCDKIWKIIKEISKDKRSECSDEY
TDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIF
DVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGL
NENEKDEIEELVSQIIQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0000067goblet cell
PLANA:0000240body wall musculature
PLANA:0000418head
PLANA:0000419prepharyngeal region
PLANA:0000420parapharyngeal region
PLANA:0002075pigment cell
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 144..164
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..17
score: 0.69