SMED30029207

Overview
NameSMED30029207
Smed IDSMED30029207
Length (bp)1515
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 SMED30029207 (SMED30029207) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029207 (SMED30029207) 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.
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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



SMED30029207

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30029207 Contig1681newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30029207 Contig1681newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30029207 Contig1681newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30029207 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000053:35870..37428 +7079
Homology
[Close]
BLAST of SMED30029207 vs. Planmine SMEST
Match: SMESG000034272.1 (SMESG000034272.1)

HSP 1 Score: 106.301 bits (264), Expect = 3.150e-25
Identity = 69/118 (58.47%), Postives = 83/118 (70.34%), Query Frame = -1 
Query: 1105 TGDSCGYVIVWXXXXXXXXXXXXKSPETSGIMEFKLIIDXPSKEEFFIISSKAVSVQ*FSIVELFDENSSKMLLAFYNKVEVCRCNRFNVILNWNTSYVI*RGIYKQSREECNERNEF 1458
            +GD CGYVIVW + FDE+KFIKFKS E S I++FK +ID  SKEEF  I  K  +VQ FSI  L DE+SS+ML  FYN+ + C CN FNVIL  NTS V+  G  +QS EEC+ RNE 
Sbjct:  108 SGDLCGYVIVWKLIFDEMKFIKFKSIEVSEIIDFKWMIDSSSKEEFLYICDKTGTVQSFSIGNLSDESSSEMLSTFYNQGKGCCCNGFNVILTGNTSAVLYGGSCEQSHEECSNRNEL 225

HSP 2 Score: 28.4906 bits (62), Expect = 3.150e-25
Identity = 15/40 (37.50%), Postives = 18/40 (45.00%), Query Frame = -2 
Query: 1050 EMNLFDINTYNMI------------------GTGFTTNKF 1115
            E+NL D+NTYNM+                  G GF TNK 
Sbjct:  224 ELNLCDVNTYNMVKIDLNSIANEEEDNDEGLGAGFATNKL 263
[Close]
BLAST of SMED30029207 vs. Planmine SMEST
Match: SMESG000034272.1 (SMESG000034272.1)

HSP 1 Score: 105.916 bits (263), Expect = 3.395e-25
Identity = 69/118 (58.47%), Postives = 83/118 (70.34%), Query Frame = -1 
Query: 1105 TGDSCGYVIVWXXXXXXXXXXXXKSPETSGIMEFKLIIDXPSKEEFFIISSKAVSVQ*FSIVELFDENSSKMLLAFYNKVEVCRCNRFNVILNWNTSYVI*RGIYKQSREECNERNEF 1458
            +GD CGYVIVW + FDE+KFIKFKS E S I++FK +ID  SKEEF  I  K  +VQ FSI  L DE+SS+ML  FYN+ + C CN FNVIL  NTS V+  G  +QS EEC+ RNE 
Sbjct:   88 SGDLCGYVIVWKLIFDEMKFIKFKSIEVSEIIDFKWMIDSSSKEEFLYICDKTGTVQSFSIGNLSDESSSEMLSTFYNQGKGCCCNGFNVILTGNTSAVLYGGSCEQSHEECSNRNEL 205

HSP 2 Score: 28.4906 bits (62), Expect = 3.395e-25
Identity = 15/40 (37.50%), Postives = 18/40 (45.00%), Query Frame = -2 
Query: 1050 EMNLFDINTYNMI------------------GTGFTTNKF 1115
            E+NL D+NTYNM+                  G GF TNK 
Sbjct:  204 ELNLCDVNTYNMVKIDLNSIANEEEDNDEGLGAGFATNKL 243
[Close]
BLAST of SMED30029207 vs. Planmine SMEST
Match: SMESG000020886.1 (SMESG000020886.1)

HSP 1 Score: 72.4034 bits (176), Expect = 5.978e-15
Identity = 41/77 (53.25%), Postives = 53/77 (68.83%), Query Frame = -1 
Query: 1105 SKEEFFIISSKAVSVQ*FSIVELFDENSSKMLLAFYNKVEVCRCNRFNVILNWNTSYVI*RGIYKQSREECNERNEF 1335
            SK++  ++    +SVQ FSI +L DE+ SKML  FYN+V+VCRC+  NVILN NTS V    I +QSR ECN RN+ 
Sbjct:    5 SKKDLSVV---KLSVQSFSIGDLSDESLSKMLSPFYNQVKVCRCDGSNVILNGNTSAVHYGEICEQSRGECNNRNKL 78
The following BLAST results are available for this feature:
BLAST of SMED30029207 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 SMED30029207 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 SMED30029207 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 SMED30029207 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 SMED30029207 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 SMED30029207 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 SMED30029207 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 SMED30029207 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 SMED30029207 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 SMED30029207 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 SMED30029207 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 SMED30029207 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 SMED30029207 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 SMED30029207 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000034272.13.150e-2558.47SMESG000034272.1[more]
SMESG000034272.13.395e-2558.47SMESG000034272.1[more]
SMESG000020886.15.978e-1553.25SMESG000020886.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029207 ID=SMED30029207|Name=SMED30029207|organism=Schmidtea mediterranea sexual|type=transcript|length=1515bp
TTAATTCTTGTTACGAAAAAGCAGGTAATTTGCAATTATATTATGATATT
AGCTTTCATTCGTGTTTTAAATATGTAGAATATTATATAACTAAGGACAA
CATTTATTATTTTATNTNTNCNNANNTCAAAATCAAAACATTATATAATT
TTACTAATTCATTACCGTTATTAAATGACATCAGTATTACACCAACTGCG
GTCGAATTTGAGCAGAGATGAGATATTTTGTTATGATTTCTGGACCAATA
GAAAGTCTCGTTATATTAATTCATAAGTGGTGCAATAAATGTATTCATTG
TGGTAGTGTCTTTGTTGTTCGTGTACTAGACAGGGATTCTGTCGAATATG
CATATTTTTTTTCCATTAACATGACCCATAATGCATGTATATAATCTCGT
TTCAAAGCATAAATTAATGACAATAAGATTATACTTGGATTCCAAGATTT
TATCATAATGAATGTAAGCAACAAAACATCAAAAATTTCTTGACGCTCAT
CATTTTCTGAAGCAAAATTTCGATCGATTGTTTATTGCAACAAACGAGTT
TGGTAGAAGATGATTTAATTACAATAAAAGAAGGATGGGTCATTTATGTT
GAAAACTGTCCATAATTTATCACATGATTATTATAAAGTTACATTGACGC
AAAAAAACAGAATTTCAAATATATAATATAAAAACTATTGTATTGCAAAT
AACTGGATACAACATGGCATTCCAAACGCCGATATAATGTGCATAACATG
TCGTATGATCTTTGATAAGTTAGCAATTCTATAATTACAGTTATATTGTT
ATAGCGCCCAACTTATTTATAAAAGTTAAAATAACATGTTAAGTTACCAG
TTTTTAAGTTTCAATGATAGCAAGTATAACAAAATGTCCAACATTGATTC
TTGATCGATATCTGTTATCTACACCAAGCCGCATTCAAAATCAATAATGT
TATAACATAGACACACCAACTGATAATTTCTGTCTTTTCCGCAACTTTAG
TGATTTCTGTAATTTCATCAAATTCTATAACTTCGNTGGTCACTGTTATA
AATTTATTGGTGGTAAATCCGGTTCCAATCATGTTATAAGTATTAATATC
AAATAAATTCATTTCTTTCGTTACATTCTTCGCGAGATTGCTTATATATC
CCACGTTAAATCACATAAGAAGTATTCCAATTCAGAATGACATTGAATCT
ATTACATCGACAGACTTCCACTTTATTATAAAATGCTAACAACATTTTCG
ATGAGTTTTCATCAAATAACTCTACAATTGAAAACTATTGGACAGATACA
GCTTTACTAGAAATAATGAAGAATTCTTCTTTAGATGGCGNATCAATAAT
CAACTTAAATTCCATAATTCCTGAAGTTTCAGGTGATTTGAATTTAATAA
ACTTAATTTCATCAAAATNTATTTNCCATACAATTACATAACCACACGAA
TCGCCAGTATTTTNANAANNNNTNNNNTANTTNTATAAAATATGGAGTGA
CAAGATCGGAAGAGC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000418head