SMED30002800

Overview
NameSMED30002800
Smed IDSMED30002800
Length (bp)411
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30002800 (SMED30002800) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002800 (SMED30002800) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30002800

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30002800 dd_Smed_v4_62730_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002800 dd_Smed_v4_62730_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30002800 dd_Smed_v4_62730_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30002800 dd_Smed_v4_62730_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002800 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011250:15839..16243 -1837
Homology
BLAST of SMED30002800 vs. Planmine SMEST
Match: SMESG000034377.1 (SMESG000034377.1)

HSP 1 Score: 115.161 bits (287), Expect = 3.761e-32
Identity = 53/113 (46.90%), Postives = 75/113 (66.37%), Query Frame = 1
Query:   10 FGVGGLMDSFPWERQILKTMHYNYFSIIGDSSLSRSFIINVSFDRCVNDIGVILVFTALDTCNYNIDFPTDPSSYPQISYAVSDGKPANWKRYIQAAKSIEIIGRYQSNIILY 348
            F    L+DSFPW   +LK   YNYFSI GD + +RSF++N  +  C ND+GV++VF   + CNY + + T  + YPQI YA  +G P+N+  Y++ AKS+EIIG Y SNI ++
Sbjct:  171 FASTNLIDSFPWNINVLKNSTYNYFSINGDKTYNRSFLVNSQYGGCPNDVGVLMVFDGHNVCNYQLMWLTSATEYPQIIYAELNGSPSNYNNYVRVAKSLEIIGTYPSNIGIF 283          
BLAST of SMED30002800 vs. Planmine SMEST
Match: SMESG000076443.1 (SMESG000076443.1)

HSP 1 Score: 114.775 bits (286), Expect = 6.014e-32
Identity = 52/113 (46.02%), Postives = 75/113 (66.37%), Query Frame = 1
Query:   10 FGVGGLMDSFPWERQILKTMHYNYFSIIGDSSLSRSFIINVSFDRCVNDIGVILVFTALDTCNYNIDFPTDPSSYPQISYAVSDGKPANWKRYIQAAKSIEIIGRYQSNIILY 348
            F    L+DSFPW   +LK   YNYFSI GD + +RSF++N  +  C ND+GV+++F   + CNY + + T  + YPQI YA  +G P+N+  Y++ AKS+EIIG Y SNI ++
Sbjct:  171 FASTNLIDSFPWNINVLKNSTYNYFSINGDKTYNRSFLVNSQYGGCPNDVGVLMMFDGHNVCNYRLTWLTSATEYPQIIYAELNGSPSNYNNYVRVAKSLEIIGTYPSNIGIF 283          
BLAST of SMED30002800 vs. Planmine SMEST
Match: SMESG000034453.1 (SMESG000034453.1)

HSP 1 Score: 113.62 bits (283), Expect = 1.019e-31
Identity = 57/117 (48.72%), Postives = 75/117 (64.10%), Query Frame = 1
Query:    1 SDLFGVGGLMDSFPWERQILKTMHYNYFSIIGDSSLSRSFIINVSFDRCVNDIGVILVFTALDTCNYNIDFPTDPSSYPQISYAVSDGKPANWKRYIQAAKSIEIIGRYQSNIILYA 351
            S  F  G LMDSFPW++  L    Y +FSI+GD   + SF I ++   C  ++GV+LV++  + CN + D+      YPQI YAVSDG PAN  +YI  AKSIEIIGRY SN+ +YA
Sbjct:  151 SSWFNAGNLMDSFPWKKTSLIKKSYRFFSILGDKFRAISFYIILNDSMCRFEVGVLLVYSKDEQCNCDRDYIAKLKGYPQIKYAVSDGDPANLNKYINEAKSIEIIGRYPSNVTIYA 267          
BLAST of SMED30002800 vs. Planmine SMEST
Match: SMESG000076267.1 (SMESG000076267.1)

HSP 1 Score: 112.079 bits (279), Expect = 4.408e-31
Identity = 52/114 (45.61%), Postives = 77/114 (67.54%), Query Frame = 1
Query:   10 FGVGGLMDSFPWERQILKTMHYNYFSIIGDSSLSRSFIINVSFDRCVNDIGVILVFTALDTCNYNIDFPTDPSSYPQISYAVSDGKPANWKRYIQAAKSIEIIGRYQSNIILYA 351
            F +G L+DSFPW+  +LK   Y +FS+ GD    RSF I++ ++ C  D GV+++F   D C+YN+ + T   +YPQI YAV +G PA +  YI++AKS+EIIG Y S+I++Y 
Sbjct:  156 FTLGNLLDSFPWDINVLKNSLYKFFSVTGDRKGLRSFFISIRYNGCTGDAGVLMMFDGSDACSYNLKWITSAINYPQIFYAVLNGSPAIFYNYIRSAKSLEIIGSYPSDILIYG 269          
BLAST of SMED30002800 vs. Planmine SMEST
Match: SMESG000034379.1 (SMESG000034379.1)

HSP 1 Score: 110.153 bits (274), Expect = 1.046e-30
Identity = 52/117 (44.44%), Postives = 77/117 (65.81%), Query Frame = 1
Query:    1 SDLFGVGGLMDSFPWERQILKTMHYNYFSIIGDSSLSRSFIINVSFDRCVNDIGVILVFTALDTCNYNIDFPTDPSSYPQISYAVSDGKPANWKRYIQAAKSIEIIGRYQSNIILYA 351
            S  F +G L++SFPW+  +LKT  YN+FSI+GD +L RSF I+  +  C  D+GV+++F A D C Y + +    + YPQI YAV +G PA +   ++ AKS+EIIG Y  N+ +Y+
Sbjct:  113 SSWFILGNLLNSFPWDTNMLKTKTYNFFSIVGDRTLFRSFFIHSYYGGCDADVGVLMIFDAPDACEYGLAWIVQLNKYPQIIYAVKNGMPALYNDNVRQAKSLEIIGVYSQNVEIYS 229          
The following BLAST results are available for this feature:
BLAST of SMED30002800 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 SMED30002800 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 SMED30002800 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 SMED30002800 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 SMED30002800 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 SMED30002800 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 SMED30002800 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 SMED30002800 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 SMED30002800 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 SMED30002800 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 SMED30002800 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 SMED30002800 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 SMED30002800 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 SMED30002800 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000034377.13.761e-3246.90SMESG000034377.1[more]
SMESG000076443.16.014e-3246.02SMESG000076443.1[more]
SMESG000034453.11.019e-3148.72SMESG000034453.1[more]
SMESG000076267.14.408e-3145.61SMESG000076267.1[more]
SMESG000034379.11.046e-3044.44SMESG000034379.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002800 ID=SMED30002800|Name=SMED30002800|organism=Schmidtea mediterranea sexual|type=transcript|length=411bp
TCCGATCTGTTCGGTGTCGGCGGTTTGATGGATTCCTTTCCTTGGGAAAG
ACAAATTTTAAAAACAATGCATTATAACTATTTTAGTATCATCGGGGACA
GTTCCCTCTCTAGATCCTTCATCATCAATGTATCATTCGATAGATGTGTT
AATGATATAGGGGTAATTCTGGTGTTTACTGCGCTTGATACCTGCAATTA
TAACATCGATTTTCCAACCGACCCAAGCAGTTACCCACAGATATCCTACG
CAGTCTCTGACGGAAAACCGGCAAATTGGAAAAGGTATATTCAGGCAGCA
AAGTCTATAGAAATAATTGGAAGGTATCAGTCTAACATAATCCTTTACGC
ATGATTTGCAAATAATTGTTTGCACTAAAAACAGATCTTTGTCTAACAGA
TTTATTTTGAG
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protein sequence of SMED30002800-orf-1

>SMED30002800-orf-1 ID=SMED30002800-orf-1|Name=SMED30002800-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=118bp
SDLFGVGGLMDSFPWERQILKTMHYNYFSIIGDSSLSRSFIINVSFDRCV
NDIGVILVFTALDTCNYNIDFPTDPSSYPQISYAVSDGKPANWKRYIQAA
KSIEIIGRYQSNIILYA*
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