SMED30004673

Overview
NameSMED30004673
Smed IDSMED30004673
Length (bp)525
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 SMED30004673 (SMED30004673) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004673 (SMED30004673) 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 SMED30004673 (SMED30004673) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004673 (SMED30004673) 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



SMED30004673

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



PAGE Curations: 42

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig12906uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig12906newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig11365uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig11365newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig3803newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig3803uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001401 Contig3803newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001401 Contig3803uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig16231newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig16231uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig15215uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig15215newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig18824uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig18824newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig8362newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig8362uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30004673h1SMcG0001857 dd_Smed_v4_2745_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30004673h1SMcG0001857 dd_Smed_v4_2745_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30004673h1SMcG0001857 dd_Smed_v4_2745_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30004673h1SMcG0001857 dd_Smed_v4_2745_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig4552uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig4552newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig6638newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig6638uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
gutSMED30004673h1SMcG0001857 dd_Smed_v4_12181_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30004673h1SMcG0001857 dd_Smed_v4_12181_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig5813uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0001857 Contig5813newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0017953 Contig4552uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0017953 Contig4552newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0021391 Contig5813uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004673h1SMcG0021391 Contig5813newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
cephalic gangliaSMED30004673 dd_Smed_v4_10763_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30004673h1SMcG0001857 dd_Smed_v6_2745_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30004673h1SMcG0001857 dd_Smed_v6_2745_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
oocyteSMED30004673h1SMcG0001857 Contig16231newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30004673h1SMcG0001857 Contig16231uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30004673h1SMcG0001857 Contig16231newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30004673h1SMcG0001857 Contig16231uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
epidermisSMED30004673h1SMcG0001857 dd_Smed_v4_2745_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30004673h1SMcG0001857 dd_Smed_v4_2745_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30004673h1SMcG0001857 dd_Smed_v4_12181_1_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
Homology
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BLAST of SMED30004673 vs. Planmine SMEST
Match: SMESG000074957.1 (SMESG000074957.1)

HSP 1 Score: 203.756 bits (517), Expect = 2.347e-68
Identity = 99/110 (90.00%), Postives = 103/110 (93.64%), Query Frame = 1 
Query:   82 MNHIFKGFIYFAIILNIASQEIPQPYCIKSKPFMKKDRTCADFNDICVKNGDQECEHFKTACQQCPPTNFSVIMFQDILYLKKELVGVKYLIQNQMDKQIRNFRLELDRF 411
            MNHIFKGFIYFAIIL IASQE+P  YC+  KPFMKKDRTCADFNDIC+K GDQECEHFKTACQQCPPTNFSVIMFQDILYLKKELVGVKYLIQNQMDKQIRNFRLEL +F
Sbjct:    1 MNHIFKGFIYFAIILIIASQELP--YCVIEKPFMKKDRTCADFNDICLKIGDQECEHFKTACQQCPPTNFSVIMFQDILYLKKELVGVKYLIQNQMDKQIRNFRLELGKF 108
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BLAST of SMED30004673 vs. Planmine SMEST
Match: SMESG000074956.1 (SMESG000074956.1)

HSP 1 Score: 97.0561 bits (240), Expect = 1.074e-23
Identity = 78/151 (51.66%), Postives = 100/151 (66.23%), Query Frame = 1 
Query:  103 FIYFAIILNIASQEIPQPYCIKSKPFMKKDRTCADFNDICVKNGDQECEHFKTACQQCPPTNFSVIMFQDILYLKKELVGVKYLIQN--------QMDKQIRNFRL--ELDRFRNFSVTXXXXXXXXXXXXXXXXXEIRFKLISKLFRNIT 525
             I+F  +L IA  E P+  CI   PF K D +C +F  ICVK  D  C++F +AC+QCPPTN++VIM+QD+L +K E++  K  I N         ++K+ +  ++    D  RN SV IIIL SLILILSILSILEIRFKLISKLFRNIT
Sbjct:    7 LIFFLSVL-IAHTETPKNTCIIDYPFRKDDFSCDNFEKICVKTDDDVCKNFLSACKQCPPTNYTVIMYQDLLKIKDEILIAKNEILNLTVIFNKTNLNKEAKLNKILKSGDLIRNVSVAIIILHSLILILSILSILEIRFKLISKLFRNIT 156
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BLAST of SMED30004673 vs. Planmine SMEST
Match: SMESG000074945.1 (SMESG000074945.1)

HSP 1 Score: 85.5001 bits (210), Expect = 5.420e-20
Identity = 36/91 (39.56%), Postives = 59/91 (64.84%), Query Frame = 1 
Query:  103 FIYFAIILNIASQEIPQPYCIKSKPFMKKDRTCADFNDICVKNGDQECEHFKTACQQCPPTNFSVIMFQDILYLKKELVGVKYLIQNQMDK 375
            FI+    +  A  E P+  C   K F   D +CAD+ND+C+K GD +C +F+TAC QCPP+N+S++M+ D++ +K +++  K  ++N  DK
Sbjct:    6 FIFLLSGVICAGGEKPRFICQNPKSFRTNDNSCADYNDVCIKTGDPDCANFQTACNQCPPSNYSIMMYIDMMNMKNQIIISKSQMKNLTDK 96
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BLAST of SMED30004673 vs. Planmine SMEST
Match: SMESG000074941.1 (SMESG000074941.1)

HSP 1 Score: 83.5741 bits (205), Expect = 5.296e-19
Identity = 35/70 (50.00%), Postives = 48/70 (68.57%), Query Frame = 1 
Query:  139 QEIPQPYCIKSKPFMKKDRTCADFNDICVKNGDQECEHFKTACQQCPPTNFSVIMFQDILYLKKELVGVK 348
             EIP+ +C    PF  KD  C DF ++CVK  D EC +F+T C+QCPP+N+SV+MF D+L +K EL+  K
Sbjct:   18 HEIPRSHCPIGSPFKTKDNLCKDFYEVCVKQNDLECLNFQTICKQCPPSNYSVLMFMDLLTVKNELIKTK 87
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BLAST of SMED30004673 vs. Planmine SMEST
Match: SMESG000074941.1 (SMESG000074941.1)

HSP 1 Score: 83.5741 bits (205), Expect = 5.374e-19
Identity = 35/70 (50.00%), Postives = 48/70 (68.57%), Query Frame = 1 
Query:  139 QEIPQPYCIKSKPFMKKDRTCADFNDICVKNGDQECEHFKTACQQCPPTNFSVIMFQDILYLKKELVGVK 348
             EIP+ +C    PF  KD  C DF ++CVK  D EC +F+T C+QCPP+N+SV+MF D+L +K EL+  K
Sbjct:   18 HEIPRSHCPIGSPFKTKDNLCKDFYEVCVKQNDLECLNFQTICKQCPPSNYSVLMFMDLLTVKNELIKTK 87
The following BLAST results are available for this feature:
BLAST of SMED30004673 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 SMED30004673 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 SMED30004673 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 SMED30004673 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 SMED30004673 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 SMED30004673 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 SMED30004673 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 SMED30004673 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 SMED30004673 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 SMED30004673 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 SMED30004673 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 SMED30004673 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 SMED30004673 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 SMED30004673 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000074957.12.347e-6890.00SMESG000074957.1[more]
SMESG000074956.11.074e-2351.66SMESG000074956.1[more]
SMESG000074945.15.420e-2039.56SMESG000074945.1[more]
SMESG000074941.15.296e-1950.00SMESG000074941.1[more]
SMESG000074941.15.374e-1950.00SMESG000074941.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004673 ID=SMED30004673|Name=SMED30004673|organism=Schmidtea mediterranea sexual|type=transcript|length=525bp
TATGCAATATTCAATGTTTCTACAATTGATATGAATTTACACAAGCAAAA
AAACTGCAAAAATTTTAACTTAAAGTTAGATATGAATCATATTTTTAAAG
GATTTATCTATTTTGCAATTATTCTCAATATTGCATCACAAGAAATTCCA
CAACCATATTGCATCAAAAGTAAACCATTTATGAAAAAAGACAGAACTTG
TGCGGATTTCAATGATATTTGTGTCAAAAATGGAGATCAGGAATGCGAAC
ATTTCAAGACAGCGTGCCAGCAATGCCCGCCGACGAATTTCAGCGTAATC
ATGTTTCAGGATATTTTATATTTGAAGAAAGAATTGGTCGGTGTAAAATA
TCTAATTCAAAATCAGATGGATAAACAAATTCGCAACTTCCGATTGGAAT
TAGATCGGTTCAGAAATTTTTCTGTCACAATTATTATTTTGCTATCCCTG
ATCCTGATCCTCTCGATCCTCTCGATCCTGGAAATCAGATTCAAATTAAT
CTCTAAATTATTTCGGAACATCACT
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protein sequence of SMED30004673-orf-1

>SMED30004673-orf-1 ID=SMED30004673-orf-1|Name=SMED30004673-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=175bp
YAIFNVSTIDMNLHKQKNCKNFNLKLDMNHIFKGFIYFAIILNIASQEIP
QPYCIKSKPFMKKDRTCADFNDICVKNGDQECEHFKTACQQCPPTNFSVI
MFQDILYLKKELVGVKYLIQNQMDKQIRNFRLELDRFRNFSVTIIILLSL
ILILSILSILEIRFKLISKLFRNIT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000034epidermis