SMED30008821

Overview
NameSMED30008821
Smed IDSMED30008821
Length (bp)1527
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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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Alignments
SMED30008821 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.017882:9924..11415 -5882
v31.016137:4593..6497 -4855
Homology
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BLAST of SMED30008821 vs. TrEMBL
Match: A0A2C9L5J0 (Uncharacterized protein OS=Biomphalaria glabrata OX=6526 GN=106061778 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 6.046e-8
Identity = 28/69 (40.58%), Postives = 39/69 (56.52%), Query Frame = -2 
Query:   87 SIELPAHSHNLVLCDFFIWSYLKDIIYKEKVATIEELWEYITILCTEISTKIYDNACESVIQRIKNCRD 293
             IE PA S +L   DFF+W  +KD++YK K+  ++ LW  I  +C EIS        ESV+ R + C D
Sbjct:   58 PIEFPARSPDLTPLDFFLWGTVKDVVYKRKLRHLDTLWNEIQAVCAEISVDTLVRCTESVLTRTQQCID 126
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BLAST of SMED30008821 vs. TrEMBL
Match: A0A154PKV9 (Uncharacterized protein OS=Dufourea novaeangliae OX=178035 GN=WN55_04312 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 3.212e-6
Identity = 25/67 (37.31%), Postives = 40/67 (59.70%), Query Frame = -2 
Query:   93 SIELPAHSHNLVLCDFFIWSYLKDIIYKEKVATIEELWEYITILCTEISTKIYDNACESVIQRIKNC 293
            S+  PA S +L  CDFF+W +LK I+++  V  +  L   IT  CTEI+ ++  N   + I+R++ C
Sbjct:   82 SVNWPARSPDLSSCDFFLWGHLKGIVFQTPVENLNNLRRRITNACTEITQEMLKNTEAAFIRRLEKC 148
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BLAST of SMED30008821 vs. TrEMBL
Match: A0A2P8Z2Z7 (Uncharacterized protein OS=Blattella germanica OX=6973 GN=C0J52_12752 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 3.518e-6
Identity = 27/70 (38.57%), Postives = 43/70 (61.43%), Query Frame = -2 
Query:   81 IELPAHSHNLVLCDFFIWSYLKDIIYKEKVATIEELWEYITILCTEISTKIYDNACESVIQRIKNCRDES 290
            +E P  S +L +CD+F+W YLK  +Y EK+ T+E L E IT    EIS  + D   +++  R++ C D++
Sbjct:    9 LEWPPRSPDLSVCDYFLWGYLKSRVYIEKLRTLEVLAESITREVREISLSMLDRCMDNLSTRLQQCLDKN 78
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BLAST of SMED30008821 vs. TrEMBL
Match: E2AGZ7 (Transposable element Tc3 transposase (Fragment) OS=Camponotus floridanus OX=104421 GN=EAG_00323 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 4.321e-6
Identity = 25/67 (37.31%), Postives = 41/67 (61.19%), Query Frame = -2 
Query:   81 PAHSHNLVLCDFFIWSYLKDIIYKEKVATIEELWEYITILCTEISTKIYDNACESVIQRIKNCRDES 281
            PA S +L   DFF+W  LK+++YKE+  T + + + I   CT I+  +   A +S+I RI++C D +
Sbjct:   92 PARSPDLTPLDFFLWGTLKNMVYKEEPTTPQAMQQQIITACTLITPNVIKRATQSLIGRIQSCIDNT 158
The following BLAST results are available for this feature:
BLAST of SMED30008821 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 SMED30008821 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 SMED30008821 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 SMED30008821 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 SMED30008821 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 SMED30008821 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 SMED30008821 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 SMED30008821 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A2C9L5J06.046e-840.58Uncharacterized protein OS=Biomphalaria glabrata O... [more]
A0A154PKV93.212e-637.31Uncharacterized protein OS=Dufourea novaeangliae O... [more]
A0A2P8Z2Z73.518e-638.57Uncharacterized protein OS=Blattella germanica OX=... [more]
E2AGZ74.321e-637.31Transposable element Tc3 transposase (Fragment) OS... [more]
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BLAST of SMED30008821 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 SMED30008821 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 SMED30008821 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 SMED30008821 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 SMED30008821 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 SMED30008821 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008821 ID=SMED30008821|Name=SMED30008821|organism=Schmidtea mediterranea sexual|type=transcript|length=1527bp
ACTTAATGTGTCAAATATAGTTTTTATATTATAATTATGTATAAATTTAT
TAATACAAAAAAATATTCCTATTAACATCAACTCTCATCACGACAGTTCT
TTATTCTTTGGATTACACTTTCGCATGCATTGTCGTAAATTTTGGTTGAT
ATCTCTGTGCATAATATAGTAATATATTCCCAAAGCTCTTCAATTGTAGC
TACTTTCTCTTTATATATAATATCCTTCAGGTAGCTCCAAATAAAGAAAT
CGCAGAGAACTAAGTTATGAGAATGTGCCGGCAACTCGATTGACCACGTC
TACCAATTCAGGTAACTTCTTGTCGATACATTGTGACATACTGAGCTTAT
GCTGCATTCAGTTGAAAGTATATATCCTTGCACCTTATTTTTTGCCCAAA
GAAAGTTTGTGAGCATGGCCAGTAAATGTGAGTGTTCACATTTTTCTAGA
AGTAAGGTTCGATTATGCCTTTTGTGTAACCGGGATTTGTACGTGTATCG
TATAAATATCGTATAGTTTTAGCTTGTGGATACTCACTAGGGAATTGAAT
TTTCCATTGACGTCGGAATTTCCAAATTTGGCAAGTAATTGAATTATTTT
GATTCAATCTTCTAGACTTAATCGTGAATACATGAGTTTTATATCCATTC
AAGTACTTTCATGTATTTTTAAAAACATTGACTTTTGGTTAATAGATTAT
GTTAATATACTGACTACCTATAAAACACCCTGTAGATAACGCATATTTTA
CCTTCTAAAAATTATGTCTCATATATGTTAAATTTTTCAACCTAATTTAA
CATACCTTATAACAGCTCTTATAGTATAATCAATTCTTTTTTACTGGTTT
AGTAAATATTCGCTGTTTATTTGAAAGTGTTAGTTAGACCTGCACGTTAT
ATGCTTAAAAATACGATATATTTTTTATTTTAATAAATTTATTATTATTT
CCCGAAATATATTTTTCTCATAAACTCAGCAGAACATCGACGTACTAAAA
TATATTTTACCTGATTTGTTCTTATGTTAATTTAGAAAAATACAATTCTT
ATTGAATGTACAGTTTAATATGTACAAAGAGAGGGAAAAGCTAAAAATTA
TTAAAATACAGTTAAACATTAGTAGGTATGAGATATCCGACATTTAATTT
GGAATTAATTAATTAANTATAATAAACTAAACCCTTTTGTTTAGAGAAAC
ATATCTAGTAAGTTTTAATGTTTGTAATTAGTTTTATCAAAACGAAAACT
AAACATTTTAGTCTCAATAATGATGCGGTCTATAATAATTATCTTGTGTG
GATTTGCACTAACTGTGGACAATTCTGTGGGGATAATAATTTCCCAATTT
CATTTATAATAGATTTAAGGTGACTTTAAATTATATGCGAAACAATAGAG
AGGGGAATAATAGAAGAAGAATATTCAACAACCCTACACTCCCAAACTAT
CAGACATTCAATTAGCCTTTAATGATGCTAATTTATTATTATTCGTGTCG
ACATTATTAATAATAATTTCATTATTG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 4..26