SMED30009994

Overview
NameSMED30009994
Smed IDSMED30009994
Length (bp)1681
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 SMED30009994 (SMED30009994) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009994 (SMED30009994) 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 SMED30009994 (SMED30009994) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009994 (SMED30009994) 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



SMED30009994

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30009994SMESG000077592.1 Contig4299newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30009994SMESG000077592.1 Contig4299uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30009994SMESG000048581.1 Contig4299newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30009994SMESG000048581.1 Contig4299uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
X1 cellSMED30009994SMESG000077592.1 SmedASXL_014876SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30009994SMESG000077592.1 Contig55592newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009994 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000703:59638..61379 +8312
Homology
[Close]
BLAST of SMED30009994 vs. Planmine SMEST
Match: SMESG000077592.1 (SMESG000077592.1)

HSP 1 Score: 1052.74 bits (2721), Expect = 0.000e+0
Identity = 544/549 (99.09%), Postives = 547/549 (99.64%), Query Frame = 1 
Query:   19 MSVKNAKKSTNVDSSKSSKIKMVKNLNIKPDCXXXXXXXXXXXXXXXXMQIKTQNQVLIKDIEHLLSNKKEWTEKDLEKLFSIMYYPSEVASIYGFQIEKGILEYIDSAYSFKSIQLSALCLSRFANIKKSNGALLLQRVLKTLLNIGKEYFDFFDISSNLIELTYDFPVPLLNFPEIVISNETISILIKRINFLFGVIYFTFDIKNELSLPNIFDDLVRMFFAFLSITPGELLCKKMQESSMIMSIPNTVNSNLWKILNCVFLSLGFNHIEYVPKMCGIIKLCLLDDLIGNDLSYNLYIENILIFLSNIIGNGCVYCLSSVNPLIQFVVQRINAIVSLACTNSQEHILTLYLQILNKFLSHYRDKNIEKSISNLKDSLVHIKTNLIYLNSKSIYSNNQFKAEYNLFLKSFKLCVYKSCHETGISYDYFKSENSNYQNKSSNSDEEILMESQVIDIEEIKIEDTSTMEIWKITDQCIETREVNTELPIGREPVVPNSIPDQETNDMCEITNVIAVEEENPDLQTDSNHLQLNDSKFMDLEEMLKSFIPI 1665
            MSVKNAKKSTNVDSSKSSK+KMVKNLNIKPDCKPNNKLNSFKKKKLKNMQIKTQNQVLIKDIEHLLSNKKEWTEKDLEKLFSIMYYPSEVASIYGFQIEKGILEYIDSAYSFKSIQLSALCLSRFANIKKSNGALLLQRVLKTLLNIGKEYFDFFDISSNLIELTYDFPVPLLNFPEIVISNETISILIKRINFLFGVIYFTFDIKNELSLPNIFDDLVRMFFAFLSITPGELLCKKMQESSMIMSIPNTVNSNLWKILNCVFLSLGFNHIEYVPKMCGIIKLCLLDDLIGNDLSYNLYIENILIFLSNIIGNGCVYCLSSVNPLIQFVVQRINAIVSLACTNSQEHILTLYLQILNKFLSHYRDKNI+KSISNLKDSLVHIKTNLIYLNSKSIYSNNQFK EYNLFLKSFKLCVYKSCHETGISYDYFKSENSNYQNKSSNSDEEILMESQVIDIEEIKIEDTSTMEIWKITDQCIETREVNTELPI REPVVPNSIPD+ETNDMCEITNVIAVEEENPDLQTDSNHLQLNDSKFMDLEEMLKSFIPI
Sbjct:    1 MSVKNAKKSTNVDSSKSSKMKMVKNLNIKPDCKPNNKLNSFKKKKLKNMQIKTQNQVLIKDIEHLLSNKKEWTEKDLEKLFSIMYYPSEVASIYGFQIEKGILEYIDSAYSFKSIQLSALCLSRFANIKKSNGALLLQRVLKTLLNIGKEYFDFFDISSNLIELTYDFPVPLLNFPEIVISNETISILIKRINFLFGVIYFTFDIKNELSLPNIFDDLVRMFFAFLSITPGELLCKKMQESSMIMSIPNTVNSNLWKILNCVFLSLGFNHIEYVPKMCGIIKLCLLDDLIGNDLSYNLYIENILIFLSNIIGNGCVYCLSSVNPLIQFVVQRINAIVSLACTNSQEHILTLYLQILNKFLSHYRDKNIQKSISNLKDSLVHIKTNLIYLNSKSIYSNNQFKVEYNLFLKSFKLCVYKSCHETGISYDYFKSENSNYQNKSSNSDEEILMESQVIDIEEIKIEDTSTMEIWKITDQCIETREVNTELPIDREPVVPNSIPDRETNDMCEITNVIAVEEENPDLQTDSNHLQLNDSKFMDLEEMLKSFIPI 549
The following BLAST results are available for this feature:
BLAST of SMED30009994 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 SMED30009994 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 SMED30009994 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 SMED30009994 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 SMED30009994 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 SMED30009994 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 SMED30009994 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 SMED30009994 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 SMED30009994 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 SMED30009994 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 SMED30009994 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 SMED30009994 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 SMED30009994 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 SMED30009994 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000077592.10.000e+099.09SMESG000077592.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009994 ID=SMED30009994|Name=SMED30009994|organism=Schmidtea mediterranea sexual|type=transcript|length=1681bp
TAAAAATTCAAGGTGAATATGAGTGTTAAAAATGCAAAAAAATCAACAAA
TGTAGATTCAAGTAAGTCAAGTAAAATTAAGATGGTAAAAAATCTAAACA
TTAAACCAGATTGTAAACCTAACAACAAACTAAACAGTTTTAAAAAGAAA
AAACTTAAAAATATGCAAATTAAAACTCAAAATCAGGTATTGATTAAGGA
CATAGAACATTTATTGTCTAATAAAAAAGAATGGACTGAAAAGGATCTTG
AAAAATTATTTTCAATAATGTATTATCCTTCTGAAGTTGCATCAATTTAC
GGTTTTCAAATTGAAAAAGGAATTTTGGAATATATTGATAGTGCGTATTC
TTTTAAATCTATTCAATTATCTGCACTATGCTTGAGTAGATTTGCTAATA
TAAAAAAATCAAATGGAGCGCTATTACTTCAAAGAGTTCTTAAAACACTG
CTGAATATTGGTAAAGAATATTTCGATTTTTTTGATATTTCATCAAATCT
AATTGAATTAACATATGACTTTCCAGTACCTCTCTTAAATTTCCCTGAAA
TTGTTATCAGTAACGAGACAATCTCAATTCTAATTAAACGAATTAATTTT
CTTTTCGGTGTGATTTATTTTACATTTGATATTAAAAATGAATTATCTCT
ACCTAATATTTTCGATGATTTAGTTCGAATGTTTTTTGCATTTCTATCTA
TTACACCTGGTGAGTTGCTGTGCAAGAAAATGCAAGAATCTTCAATGATA
ATGTCAATTCCAAATACTGTTAATTCTAATTTATGGAAAATACTTAATTG
CGTATTTTTATCATTAGGTTTTAATCATATTGAATATGTTCCGAAAATGT
GTGGAATTATTAAATTATGTCTCTTGGATGATTTAATTGGAAATGATTTA
TCATATAATTTGTATATTGAGAATATTCTGATATTTTTGTCCAATATTAT
CGGCAATGGTTGTGTTTATTGTTTGTCATCTGTGAACCCGTTGATTCAGT
TTGTTGTTCAAAGGATCAATGCGATTGTCAGTTTAGCTTGTACAAACAGT
CAAGAACATATTCTCACTCTATATTTACAAATTTTAAATAAATTTCTGTC
ACATTATCGGGACAAAAACATTGAAAAATCTATTTCGAATTTGAAAGATT
CACTGGTTCATATTAAAACAAATCTGATTTATTTAAATAGTAAATCTATC
TATTCAAACAATCAATTCAAGGCCGAATACAATCTATTCTTAAAGTCTTT
TAAGCTATGCGTTTACAAAAGTTGCCATGAGACTGGAATTTCATATGATT
ATTTCAAATCCGAAAATTCAAATTATCAGAATAAATCTAGCAATTCAGAT
GAGGAAATTTTGATGGAGTCACAAGTTATTGACATTGAAGAAATTAAGAT
AGAGGATACCTCAACAATGGAAATTTGGAAAATTACCGATCAATGTATCG
AAACACGTGAAGTCAATACAGAGTTGCCCATAGGTCGGGAACCCGTAGTT
CCGAATTCTATCCCCGATCAAGAGACTAATGACATGTGTGAAATCACAAA
TGTGATTGCAGTTGAGGAGGAGAATCCGGATTTACAGACAGATTCGAATC
ATTTACAACTCAACGATTCGAAATTTATGGATTTAGAAGAGATGCTGAAA
TCATTCATTCCCATTTAAATATATATTATTC
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protein sequence of SMED30009994-orf-1

>SMED30009994-orf-1 ID=SMED30009994-orf-1|Name=SMED30009994-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=550bp
MSVKNAKKSTNVDSSKSSKIKMVKNLNIKPDCKPNNKLNSFKKKKLKNMQ
IKTQNQVLIKDIEHLLSNKKEWTEKDLEKLFSIMYYPSEVASIYGFQIEK
GILEYIDSAYSFKSIQLSALCLSRFANIKKSNGALLLQRVLKTLLNIGKE
YFDFFDISSNLIELTYDFPVPLLNFPEIVISNETISILIKRINFLFGVIY
FTFDIKNELSLPNIFDDLVRMFFAFLSITPGELLCKKMQESSMIMSIPNT
VNSNLWKILNCVFLSLGFNHIEYVPKMCGIIKLCLLDDLIGNDLSYNLYI
ENILIFLSNIIGNGCVYCLSSVNPLIQFVVQRINAIVSLACTNSQEHILT
LYLQILNKFLSHYRDKNIEKSISNLKDSLVHIKTNLIYLNSKSIYSNNQF
KAEYNLFLKSFKLCVYKSCHETGISYDYFKSENSNYQNKSSNSDEEILME
SQVIDIEEIKIEDTSTMEIWKITDQCIETREVNTELPIGREPVVPNSIPD
QETNDMCEITNVIAVEEENPDLQTDSNHLQLNDSKFMDLEEMLKSFIPI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0002109X1 cell