SMED30031964

Overview
NameSMED30031964
Smed IDSMED30031964
Length (bp)1430
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 SMED30031964 (SMED30031964) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031964 (SMED30031964) 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




SMED30031964

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30031964SMESG000014290.1 Contig2857newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30031964SMESG000014290.1 Contig2857uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30031964 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002515:56803..58106 -4748
v31.002728:50427..51730 -4683
Homology
BLAST of SMED30031964 vs. Planmine SMEST
Match: SMESG000073893.1 (SMESG000073893.1)

HSP 1 Score: 77.7962 bits (190), Expect = 4.823e-17
Identity = 40/70 (57.14%), Postives = 45/70 (64.29%), Query Frame = 1
Query:  421 NLQLIRMRDDLISETRAQRLVISKQSRVLMTTFTETELKIRLPKTYFSRFPNILPAQDMQPKQSDKQLIL 630
            NL L R+RDDLI E   QRLVI  QS  LM+ FTETELKI L   Y    P+I+ AQ +Q KQS   LIL
Sbjct:   16 NLHLARIRDDLIVENHTQRLVIYDQSEALMSVFTETELKIWLLNIYLLWLPDIVLAQHIQTKQSINSLIL 85          
BLAST of SMED30031964 vs. Planmine SMEST
Match: SMESG000077490.1 (SMESG000077490.1)

HSP 1 Score: 78.9518 bits (193), Expect = 7.195e-17
Identity = 47/135 (34.81%), Postives = 67/135 (49.63%), Query Frame = 1
Query:  364 DRIMVTWFKPAKYKELQSTNLQLIRMRDDLISETRAQRLVISKQSRVLMTTFTETELKIRLPKTYFSRFPNILPAQDMQPKQSDKQLILPKPTTVAKPGKKSS------SSNTLTFENATKIRKMSRYSYWMN*H 750
            +R + TWF P   K L     +L R R+DLI+E RAQR+VI+ QS VL+ +FTETEL  RL     +   N++PA D+  +        PK +    P K  S      +       NA ++R + +Y    N H
Sbjct:   45 ERTLGTWFAPEVVKALHKQIHRLTRCREDLIAENRAQRIVINDQSAVLIASFTETELTKRLASRDLAVKLNLIPANDLPERNQIGPAQTPKTSKKHNPSKNRSGRERRRAEGVTLLNNAAQVRNLHKYIASHNPH 179          
BLAST of SMED30031964 vs. Planmine SMEST
Match: SMESG000071407.1 (SMESG000071407.1)

HSP 1 Score: 77.411 bits (189), Expect = 3.981e-16
Identity = 43/125 (34.40%), Postives = 72/125 (57.60%), Query Frame = 1
Query:  319 LDE*KARAKYLRQKLDRIMVTWFKPAKYKELQSTNLQLIRMRDDLISETRAQRLVISKQSRVLMTTFTETELKIRLPKTYFSRFPNILPAQDM-------QPKQSDKQLILPKPTTVAKPGKKSS 672
            L+E + + + L+ K DR+  TW  P   K L    ++L R RD+LI+E+R+QR++I +QS  L   FT+ EL+ R+P + ++R  NI+P Q +        P  S  Q++ P    VA+P  +++
Sbjct:   29 LEELEGKHETLKTKYDRVKGTWTSPEAAKGLHQKIIRLSRARDELIAESRSQRVLIKEQSTTLRQIFTDAELRARIPGSVWARHLNIIPEQHLPMDTINPTPSTSAPQIMEPPQILVAEPRARAA 153          
BLAST of SMED30031964 vs. Planmine SMEST
Match: SMESG000003594.1 (SMESG000003594.1)

HSP 1 Score: 76.2554 bits (186), Expect = 3.176e-15
Identity = 49/146 (33.56%), Postives = 75/146 (51.37%), Query Frame = 1
Query:  295 NVANNDD*LDE*KARAKY--LRQKLDRIMVTWFKPAKYKELQSTNLQLIRMRDDLISETRAQRLVISKQSRVLMTTFTETELKIRLPKTYFSRFPNILPAQDMQPKQSDKQLILPKPTTVAKPGKKSSSSNTLTFENATKIRKMSR 726
            ++ NNDD   + + R KY  L  + +R + TWF P   K L     +L R R+DLI+E RAQR+VI+ QS VL  +F ETELK RL     +   NI+PA+ +    +     +PK +    P K          E  ++++  ++
Sbjct:   21 SILNNDDKSHQ-ECRRKYDQLVVEHERTLSTWFAPEAVKALHKQIHRLTRCREDLIAENRAQRIVINNQSAVLTASFNETELKKRLAGRDLAIKLNIIPAEHVPETATTGPPQMPKTSKKHNPSKNRRRRERRRAEGVSQLKNAAQ 165          
BLAST of SMED30031964 vs. Planmine SMEST
Match: SMESG000036778.1 (SMESG000036778.1)

HSP 1 Score: 75.0998 bits (183), Expect = 4.278e-14
Identity = 50/145 (34.48%), Postives = 73/145 (50.34%), Query Frame = 1
Query:  298 VANNDD*LDE*KARAKY--LRQKLDRIMVTWFKPAKYKELQSTNLQLIRMRDDLISETRAQRLVISKQSRVLMTTFTETELKIRLPKTYFSRFPNILPAQDMQPKQSDKQLILPKPTTVAKPGKKSSSSNTLTFENATKIRKMSR 726
            + NNDD   + + R KY  L  + +R + TWF P   K L     +L R R+DLI+E RAQR+VI+ QS VL  +F ETELK RL     +   NI+PA+ +    +     +PK +    P K          E  T ++  ++
Sbjct:  585 ILNNDDKSHQ-ECRRKYEQLVVEHERTLGTWFAPEAVKALHKQIHRLTRCREDLIAENRAQRIVINNQSAVLTASFNETELKKRLAGRDLAIKLNIIPAEHVPETATTGPPQMPKISKKHNPSKNRRRRERRRAEGVTLLKNAAQ 728          
The following BLAST results are available for this feature:
BLAST of SMED30031964 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 SMED30031964 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 SMED30031964 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 SMED30031964 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 SMED30031964 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 SMED30031964 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 SMED30031964 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 SMED30031964 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 SMED30031964 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 SMED30031964 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 SMED30031964 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 SMED30031964 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 SMED30031964 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 SMED30031964 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000073893.14.823e-1757.14SMESG000073893.1[more]
SMESG000077490.17.195e-1734.81SMESG000077490.1[more]
SMESG000071407.13.981e-1634.40SMESG000071407.1[more]
SMESG000003594.13.176e-1533.56SMESG000003594.1[more]
SMESG000036778.14.278e-1434.48SMESG000036778.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031964 ID=SMED30031964|Name=SMED30031964|organism=Schmidtea mediterranea sexual|type=transcript|length=1430bp
TAAATGAAGTTCCACTTAAAATCCTTCTCGAAACACGATTTATAATCCGT
TTTCACGACGAAAATTCTCCCGTGTCAAACCAAAAAAAAATTTTTTAATA
GATAGCGATAATTAATTTTTTTTTGTTCAAAGGATTAATATAGATCCTTC
TTATCACTGCGAAAATTCTCCATTGTTTTCTTCCTTCAAAATTCGGAACT
GATACATTCCCAGAATTGTTCTGAATCTCATTATTCATAGTCGATATTTC
TCGCTATGCCTCAAAAATCTTTGGAAACCACATCTGTCGTTCAGAATGTC
GCAAATAACGACGATTAACTCGATGAGTAGAAGGCCAGAGCGAAATATTT
GCGCCAAAAGCTCGATCGAATCATGGTTACTTGGTTCAAACCTGCCAAAT
ATAAGGAACTTCAATCGACAAATCTGCAGCTTATCCGGATGAGGGACGAC
TTAATTTCCGAGACCAGAGCCCAACGTTTGGTTATCTCCAAGCAAAGTAG
GGTTCTAATGACCACATTTACGGAAACTGAACTGAAGATCCGGCTACCCA
AAACTTATTTCTCACGATTCCCAAACATCCTTCCAGCTCAAGACATGCAG
CCTAAACAATCAGACAAACAGTTGATCCTACCCAAACCAACCACTGTGGC
CAAACCAGGGAAAAAATCTTCGTCGTCGAATACACTGACTTTCGAAAATG
CGACAAAAATTAGAAAAATGTCTAGATATTCTTATTGGATGAATTAGCAC
TGAACACGTGAATTTGAGTTGAATTGAATGTAAAGTAATATATTTCATCG
TTGATTCAATAATTGTACATTTGCGAAGTATTGAATGCAGAGATATTATT
TTATATTGGAATATAAGAAAAACTAATGGCTAATATCTTTTATTGAATTA
AAATAATAATTGAAATTATTTAATTCCCATCAATAATAGTCACATAATAT
TTCTAATATTAATAATTTATAGTAACCTAGTTAATTAAAATTTTGAGGCC
ATTCCTCCCGCTGGTTACGCCAGGCTGGAAGAGGATTCTTAAAGAAAGTC
CTAAATCTCGAAGTATGAGATTTGGAATTGTCACGAAATTTCAAATTAAT
TTTAACTAGCATTTCCGTTGGCGCTGCAAGCACTGGCATAGGTTTTAGAA
GATTTTTTTATTTTTCTTCCTGTATTCCGTCTAGTTAAACATACCTCATA
AGTAGATCACCATTGTCTAACATCTTGTTACGTCGTATCATAAAAATTAT
TTCAGTTTCAGTCTATATAATGTTTTTTGAGACAATAAATGTCCACCTTG
TGCCCAATCAACAAATAGTGCAAGTGCTCAACAACTTTCTCTTCAATTAT
ATCATATGTAGTTCTTCAAATTATATAATCTGTTATGGTATTATTGGGTT
GCTCTATGACTTCTCGTGTCCTTTAGAAAT
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protein sequence of SMED30031964-orf-1

>SMED30031964-orf-1 ID=SMED30031964-orf-1|Name=SMED30031964-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
MVTWFKPAKYKELQSTNLQLIRMRDDLISETRAQRLVISKQSRVLMTTFT
ETELKIRLPKTYFSRFPNILPAQDMQPKQSDKQLILPKPTTVAKPGKKSS
SSNTLTFENATKIRKMSRYSYWMN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte