SMED30024165

Overview
NameSMED30024165
Smed IDSMED30024165
Length (bp)467
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30024165 (SMED30024165) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024165 (SMED30024165) 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.
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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



SMED30024165

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
tail regionSMED30024165 SmedASXL_079556SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30024165 Contig52160newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30024165 Contig52160uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30024165 dd_Smed_v4_2664_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30024165 dd_Smed_v4_2664_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30024165 dd_Smed_v6_2664_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
gutSMED30024165 SMED30024165smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30024165 SMED30024165smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
Category 3 cellSMED30024165 dd_Smed_v6_2664_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30024165 dd_Smed_v4_2664_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
SMED30024165 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007036:8881..9347 +2335
Homology
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BLAST of SMED30024165 vs. Planmine SMEST
Match: SMESG000029095.1 (SMESG000029095.1)

HSP 1 Score: 117.472 bits (293), Expect = 1.008e-34
Identity = 55/99 (55.56%), Postives = 68/99 (68.69%), Query Frame = 2 
Query:   59 MNTFSLVALFIVINYCQSSKTPERCSTKLAPAAKSCDLKYADLSDFCKDGYATINKVCKGVDTLNCAVKYKSFDVECSERKDIFWRLCGPIYKTYQALC 355
            M+  SL A+  ++ YC  S   E+C  +L PAAK CD KYA+  +FC  GYA INKVCKGVDT+ CA+KYK F   C ER+D FW+ CGP+YK YQ LC
Sbjct:    1 MSRISLFAIVYLVAYCHCS---EQCDRELVPAAKDCDRKYAETDNFCNGGYAKINKVCKGVDTIECALKYKKFGEACRERQDYFWKNCGPVYKIYQTLC 96
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BLAST of SMED30024165 vs. Planmine SMEST
Match: SMESG000020501.1 (SMESG000020501.1)

HSP 1 Score: 111.694 bits (278), Expect = 2.500e-32
Identity = 54/100 (54.00%), Postives = 66/100 (66.00%), Query Frame = 2 
Query:   59 MNTFSLVALFIVINYCQSSKTPERCSTKLAPAAKSCDLKYADLSDFCKDGYATINKVCKGVDTLNCAVKYKSFDVECSERKDIFWRLCGPIYKTYQALCG 358
            M+  S+ AL  VI YC  S    RC  +LAPAAK CD KYA+   FC  GYA INKVCKGVDT+ C ++YK F V+C ER++ FW  C  +YKTYQ +C 
Sbjct:    1 MSKLSIFALLFVIAYCHCSP---RCDLELAPAAKRCDKKYAETDAFCNGGYAAINKVCKGVDTIECGLEYKRFAVKCKERQNNFWNDCDQVYKTYQTVCA 97
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BLAST of SMED30024165 vs. Planmine SMEST
Match: SMESG000028420.1 (SMESG000028420.1)

HSP 1 Score: 98.2117 bits (243), Expect = 5.442e-27
Identity = 46/103 (44.66%), Postives = 64/103 (62.14%), Query Frame = 2 
Query:   59 MNTFSLVALFIVINYCQSSK---TPERCSTKLAPAAKSCDLKYADLSDFCKDGYATINKVCKGVDTLNCAVKYKSFDVECSERKDIFWRLCGPIYKTYQALCG 358
            MN  S+ ALF V+    S+K   +PE+C   L PAAK CD +Y +   FC  GY  I+K CKG D++ C V+Y     +C+E++D FW++CGP+YKTY   C 
Sbjct:    1 MNKISVYALFAVVVIVNSTKWVPSPEKCLKILTPAAKGCDSRYTETDLFCSVGYKHIDKSCKGHDSVECGVQYAKHKDDCTEKQDYFWKVCGPVYKTYSDECA 103
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BLAST of SMED30024165 vs. Planmine SMEST
Match: SMESG000061767.1 (SMESG000061767.1)

HSP 1 Score: 87.4261 bits (215), Expect = 1.380e-22
Identity = 41/105 (39.05%), Postives = 58/105 (55.24%), Query Frame = 2 
Query:   59 MNTFSLVALFIVINYCQSSK---TPERCSTKLAPAAKSCDLKYADLSDFCKDGYATINKVCKGVDTLNCAVKYKSFDVECSERKDIFWRLCGPIYKTYQALCGIP 364
            M   S+   F+ +    S+K      RCS  L PAA+ CD KY +  +FC  GY  INK CKG +T++C  ++   D +C E++DIFW LC  +Y  Y+  C  P
Sbjct:    1 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASP 105
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BLAST of SMED30024165 vs. Planmine SMEST
Match: SMESG000022139.1 (SMESG000022139.1)

HSP 1 Score: 84.7297 bits (208), Expect = 9.368e-22
Identity = 41/106 (38.68%), Postives = 57/106 (53.77%), Query Frame = 2 
Query:   59 MNTFSLVA--LFIVINYCQSSKTPE-RCSTKLAPAAKSCDLKYADLSDFCKDGYATINKVCKGVDTLNCAVKYKSFDVECSERKDIFWRLCGPIYKTYQALCGIPS 367
            M  FS++A  +F+ +        P  RC   L PA+K CD  Y +  +FC  G+A +NKVC G DT+ C   YK+F   C E++D FW  C P+Y  Y+  C  P 
Sbjct:    1 MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTTLCKEKQDNFWDECDPVYTAYRKECATPE 106
The following BLAST results are available for this feature:
BLAST of SMED30024165 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 SMED30024165 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 SMED30024165 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 SMED30024165 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 SMED30024165 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 SMED30024165 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 SMED30024165 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 SMED30024165 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 SMED30024165 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 SMED30024165 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 SMED30024165 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 SMED30024165 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 SMED30024165 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 SMED30024165 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000029095.11.008e-3455.56SMESG000029095.1[more]
SMESG000020501.12.500e-3254.00SMESG000020501.1[more]
SMESG000028420.15.442e-2744.66SMESG000028420.1[more]
SMESG000061767.11.380e-2239.05SMESG000061767.1[more]
SMESG000022139.19.368e-2238.68SMESG000022139.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024165 ID=SMED30024165|Name=SMED30024165|organism=Schmidtea mediterranea sexual|type=transcript|length=467bp
TTTTATTATAAAAAAAACAATATATTTTTATTTTAATTATAAACCACATT
TCGAGAAAATGAATACATTTTCACTAGTTGCTCTTTTTATTGTAATTAAT
TACTGCCAAAGTTCAAAAACACCAGAAAGGTGTTCAACAAAATTAGCACC
AGCAGCAAAGTCCTGCGACCTCAAGTACGCTGATTTGAGTGATTTCTGTA
AGGATGGATACGCGACCATAAATAAAGTATGCAAGGGTGTCGATACGTTG
AACTGTGCAGTTAAGTATAAAAGTTTTGATGTGGAATGTTCGGAAAGAAA
AGATATCTTTTGGAGATTATGTGGACCAATTTATAAAACCTATCAAGCTT
TATGTGGAATTCCCTCCGAAAACTAAAGAAGAAAAGCTGAAAATAGAAGG
AGGAAATTAACTTTTGAAAATTTTAAATGTGTTATTTTGAATTTTTGGTT
TAAATAAAAACCTCTTT
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protein sequence of SMED30024165-orf-1

>SMED30024165-orf-1 ID=SMED30024165-orf-1|Name=SMED30024165-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
FIIKKTIYFYFNYKPHFEKMNTFSLVALFIVINYCQSSKTPERCSTKLAP
AAKSCDLKYADLSDFCKDGYATINKVCKGVDTLNCAVKYKSFDVECSERK
DIFWRLCGPIYKTYQALCGIPSEN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000035Category 3 cell
PLANA:0000421tail
PLANA:0002032epidermal cell
PLANA:0002142parenchyma