SMED30004428

Overview
NameSMED30004428
Smed IDSMED30004428
Length (bp)974
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 SMED30004428 (SMED30004428) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004428 (SMED30004428) 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 SMED30004428 (SMED30004428) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004428 (SMED30004428) 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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Homology
BLAST of SMED30004428 vs. Planmine SMEST
Match: SMESG000047667.1 (SMESG000047667.1)

HSP 1 Score: 370.163 bits (949), Expect = 1.101e-116
Identity = 174/203 (85.71%), Postives = 181/203 (89.16%), Query Frame = 3
Query:  180 NPTGAGNVPTQTECTDEVKFILNNEYQIECKECGKVWENVRNGLNHLRLKHDFPNRTDVMVSCVRCEVPVKGAECANHIKNHKKDDKEESEAGSLVANTQDIPNESS*LSQAAIEVYLRNILKMKENQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWNRCHWIVYLANCDSKTSVILDSNNQMTLQQR 788
            NPTGAGNVPT+TECTDEVKFILNNEYQIECKECGKVWENVRNG+NHLR KHDFPNRTDVMVSCVRCEVP+KGAEC NHIKNHKKDDKEES+AGSLVANTQDIPNE                    +NQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWN+CHWIVYLANCDSKTSVILDS+NQMTLQQR
Sbjct:  427 NPTGAGNVPTETECTDEVKFILNNEYQIECKECGKVWENVRNGMNHLRQKHDFPNRTDVMVSCVRCEVPIKGAECVNHIKNHKKDDKEESQAGSLVANTQDIPNE--------------------KNQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWNKCHWIVYLANCDSKTSVILDSDNQMTLQQR 609          
BLAST of SMED30004428 vs. Planmine SMEST
Match: SMESG000031457.1 (SMESG000031457.1)

HSP 1 Score: 363.614 bits (932), Expect = 1.621e-116
Identity = 172/203 (84.73%), Postives = 180/203 (88.67%), Query Frame = 3
Query:  180 NPTGAGNVPTQTECTDEVKFILNNEYQIECKECGKVWENVRNGLNHLRLKHDFPNRTDVMVSCVRCEVPVKGAECANHIKNHKKDDKEESEAGSLVANTQDIPNESS*LSQAAIEVYLRNILKMKENQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWNRCHWIVYLANCDSKTSVILDSNNQMTLQQR 788
            NPTGAGNVPT+TECTDEVKFILNNEYQIECKECGK+WENVRNG+NHLR KHDF NRTDVMVSCVRCEVP+KGAEC NHIKNHKKDDKEES+AGSLVANTQDIPNE                    +NQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWN+CHWIVYLANCDSKTSVILDS+NQMTLQQR
Sbjct:  196 NPTGAGNVPTETECTDEVKFILNNEYQIECKECGKLWENVRNGMNHLRQKHDFINRTDVMVSCVRCEVPIKGAECINHIKNHKKDDKEESQAGSLVANTQDIPNE--------------------KNQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWNKCHWIVYLANCDSKTSVILDSDNQMTLQQR 378          
BLAST of SMED30004428 vs. Planmine SMEST
Match: SMESG000005302.1 (SMESG000005302.1)

HSP 1 Score: 219.935 bits (559), Expect = 1.560e-71
Identity = 101/107 (94.39%), Postives = 105/107 (98.13%), Query Frame = 3
Query:  180 NPTGAGNVPTQTECTDEVKFILNNEYQIECKECGKVWENVRNGLNHLRLKHDFPNRTDVMVSCVRCEVPVKGAECANHIKNHKKDDKEESEAGSLVANTQDIPNESS 500
            NPTGAGNVPT+TECTDEVKFILNNEYQIECKECGKVWENVRNG+NHLR KHDFPNRTDVMVSCVRCEVP+KGAEC NHIKNHKKDDKEES+AGSLVANTQDIPNESS
Sbjct:   75 NPTGAGNVPTETECTDEVKFILNNEYQIECKECGKVWENVRNGMNHLRQKHDFPNRTDVMVSCVRCEVPIKGAECVNHIKNHKKDDKEESQAGSLVANTQDIPNESS 181          
BLAST of SMED30004428 vs. Planmine SMEST
Match: SMESG000069571.1 (SMESG000069571.1)

HSP 1 Score: 210.69 bits (535), Expect = 4.602e-61
Identity = 96/104 (92.31%), Postives = 98/104 (94.23%), Query Frame = 3
Query:  183 PTGAGNVPTQTECTDEVKFILNNEYQIECKECGKVWENVRNGLNHLRLKHDFPNRTDVMVSCVRCEVPVKGAECANHIKNHKKDDKEESEAGSLVANTQDIPNE 494
            PTGAGNVPT+ ECTDEVKFILNNEYQ+ECKECGKVWENVRNGLNHLR KHDFPNRTD MVSCVRCEVP KGAEC NHIKNHKKDDKE SEAGSLVANTQDIPNE
Sbjct:  198 PTGAGNVPTENECTDEVKFILNNEYQLECKECGKVWENVRNGLNHLRQKHDFPNRTDAMVSCVRCEVPFKGAECTNHIKNHKKDDKEASEAGSLVANTQDIPNE 301          
BLAST of SMED30004428 vs. Planmine SMEST
Match: SMESG000051102.1 (SMESG000051102.1)

HSP 1 Score: 142.895 bits (359), Expect = 1.259e-42
Identity = 67/84 (79.76%), Postives = 73/84 (86.90%), Query Frame = 3
Query:  216 ECTDEVKFILNNEYQIECKECGKVWENVRNGLNHLRLKHDFPNRTDVMVSCVRCEVPVKGAECANHIKNHKKDDKEESEAGSLV 467
            E  +EVKFILNNEYQ+ECKECGKV E++RNGLNHLR KH FPNRTD MV+CVRCEVP+KG E  NHIKNHKKDDKE SE GSLV
Sbjct:    5 EGEEEVKFILNNEYQLECKECGKVSESIRNGLNHLRQKHGFPNRTDAMVTCVRCEVPIKGVERVNHIKNHKKDDKEASEVGSLV 88          
The following BLAST results are available for this feature:
BLAST of SMED30004428 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 SMED30004428 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 SMED30004428 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 SMED30004428 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 SMED30004428 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 SMED30004428 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 SMED30004428 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 SMED30004428 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 SMED30004428 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 SMED30004428 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 SMED30004428 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 SMED30004428 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 SMED30004428 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 SMED30004428 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000047667.11.101e-11685.71SMESG000047667.1[more]
SMESG000031457.11.621e-11684.73SMESG000031457.1[more]
SMESG000005302.11.560e-7194.39SMESG000005302.1[more]
SMESG000069571.14.602e-6192.31SMESG000069571.1[more]
SMESG000051102.11.259e-4279.76SMESG000051102.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004428 ID=SMED30004428|Name=SMED30004428|organism=Schmidtea mediterranea sexual|type=transcript|length=974bp
ATGGTGATCTCCTATTCCCTAAATTATACAAATTTATAAATAATTATAAT
AAAAAATTTCAGAACCTTCTAGATGAAAATTATTCCTTGTTTTACCAAAC
CAAAAATGCTGCAGTTTTGAAAAATAATGTCGGAAAAAATTTTAAAAGGA
ATTTACACATTGACATTCAAGCACTGACAAATCCTACTGGTGCAGGAAAT
GTACCAACACAAACCGAATGTACTGATGAAGTTAAATTCATCCTCAACAA
TGAGTACCAAATAGAATGTAAAGAGTGTGGAAAAGTGTGGGAAAACGTAA
GAAATGGACTAAACCACCTTCGTCTAAAACACGATTTCCCAAACAGAACA
GATGTTATGGTATCTTGTGTGAGATGTGAAGTACCGGTCAAAGGAGCAGA
ATGTGCAAATCACATTAAAAATCACAAAAAAGATGACAAAGAAGAAAGTG
AAGCAGGGAGTCTTGTAGCTAACACTCAAGACATCCCAAACGAAAGTAGC
TGACTATCACAAGCCGCAATCGAAGTATATCTGAGGAATATTCTGAAAAT
GAAAGAAAACCAGGAAAGGAATATTCAATATCTTGAACCTAGTACTGCGA
ATTTCCTCATAAATAGAAACCTCAGAGCATTCTATCAAAACGTCAAAATC
GAAAAGCTTATCGGATGGGAACAAGTCATCTGGCTTATACATTGGAACAG
ATGTCACTGGATTGTCTACCTAGCTAATTGCGACTCAAAAACCTCTGTTA
TCTTGGACTCTAACAACCAAATGACTTTACAGCAAAGATGTGAAAAAGAA
TGTAATTATGAAAATAAAAAAGAAAATGAACATTTTATGATTAAAATAAG
AATTCAAGGATATAAAGAAGGAAACCAGACTATTTGACCAATTTGGAAAA
TTATTGAAGCCAAATGTATTTAAATAAAATTTATTTAACTTAAATCGTCT
TAGTTTTTTTATTTTTTATCCTTG
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protein sequence of SMED30004428-orf-1

>SMED30004428-orf-1 ID=SMED30004428-orf-1|Name=SMED30004428-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=113bp
MKENQERNIQYLEPSTANFLINRNLRAFYQNVKIEKLIGWEQVIWLIHWN
RCHWIVYLANCDSKTSVILDSNNQMTLQQRCEKECNYENKKENEHFMIKI
RIQGYKEGNQTI*
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protein sequence of SMED30004428-orf-2

>SMED30004428-orf-2 ID=SMED30004428-orf-2|Name=SMED30004428-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=167bp
GDLLFPKLYKFINNYNKKFQNLLDENYSLFYQTKNAAVLKNNVGKNFKRN
LHIDIQALTNPTGAGNVPTQTECTDEVKFILNNEYQIECKECGKVWENVR
NGLNHLRLKHDFPNRTDVMVSCVRCEVPVKGAECANHIKNHKKDDKEESE
AGSLVANTQDIPNESS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002089reproductive organ
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR007087Znf_C2H2
Vocabulary: molecular function
TermDefinition
GO:0046872metal ion binding