SMED30032726

Overview
NameSMED30032726
Smed IDSMED30032726
Length (bp)1655
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 SMED30032726 (SMED30032726) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30032726 (SMED30032726) 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 SMED30032726 (SMED30032726) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30032726 (SMED30032726) 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



SMED30032726

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
X1 cellSMED30032726 SmedASXL_067337SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30032726 SmedASXL_067337SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30032726 SmedASXL_050467SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30032726 dd_Smed_v4_12204_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30032726 dd_Smed_v4_12204_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30032726 dd_Smed_v4_12204_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30032726 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001128:29977..31631 -8176
v31.000950:106186..112490 +7356
v31.006586:7800..9476 +6022
v31.000501:17995..19589 -5562
v31.004705:30953..32502 +5383
Homology
[Close]
BLAST of SMED30032726 vs. Planmine SMEST
Match: SMESG000059844.1 (SMESG000059844.1)

HSP 1 Score: 152.14 bits (383), Expect = 3.486e-63
Identity = 77/115 (66.96%), Postives = 87/115 (75.65%), Query Frame = 2 
Query: 1082 NSNTRWTDDDQTTLIIPNKFAGRHRQALWDWGYFLSTHRTPEWSYRNSN*CDEDVELPSPVIKRESESNLAREMRHEAEVAIQQFEHLKRKYRWKANFQGRRLAKINKYIASGRI 1426
            N +T W ++DQ TL IP+KFAGR+RQALWD  Y LSTH T EW YRN N  DED+EL S  IKRE   N ARE+RHEAEVA+QQF HL+RKY WKA+ Q RRL KINK IA GRI
Sbjct:   44 NPSTHWMENDQNTLTIPSKFAGRYRQALWDPRYSLSTHGTSEWPYRNKNRHDEDMELLSLAIKREPGRNPAREIRHEAEVALQQFVHLERKYHWKASLQLRRLVKINKDIAGGRI 158

HSP 2 Score: 110.153 bits (274), Expect = 3.486e-63
Identity = 54/72 (75.00%), Postives = 59/72 (81.94%), Query Frame = 3 
Query: 1425 SDGYLPEYNVSFNPEDQALLELNAPVHLALPKCLLQLDILKALTNRSGEEHAYSRRPLKRGVPQGIYGHRIT 1640
            SDGYL EYNV+FNPED A LELN PVHLALPK LLQ DIL+ALT+R+ EEHAYSRRPL R  P   YGH+IT
Sbjct:  161 SDGYLLEYNVTFNPEDPAFLELNTPVHLALPKRLLQPDILEALTDRTYEEHAYSRRPLNREAPPRNYGHKIT 232
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BLAST of SMED30032726 vs. Planmine SMEST
Match: SMESG000008335.1 (SMESG000008335.1)

HSP 1 Score: 132.88 bits (333), Expect = 7.022e-47
Identity = 65/111 (58.56%), Postives = 82/111 (73.87%), Query Frame = 2 
Query: 1094 RWTDDDQTTLIIPNKFAGRHRQALWDWGYFLSTHRTPEWSYRNSN*CDEDVELPSPVIKRESESNLAREMRHEAEVAIQQFEHLKRKYRWKANFQGRRLAKINKYIASGRI 1426
            +W D + TTL +P++FAGR+RQALWD GY +STH TPEW  R SN CDED ELPS VIKRE   N ARE+R E E  + ++E L+RKYR+ AN + RRLA+IN+ I +G I
Sbjct:   92 QWRDMESTTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQLERKYRYLANQKRRRLARINEDITNGHI 202

HSP 2 Score: 74.7146 bits (182), Expect = 7.022e-47
Identity = 37/60 (61.67%), Postives = 42/60 (70.00%), Query Frame = 3 
Query: 1425 SDGYLPEYNVSFNPEDQALLELNAPVHLALPKCLLQLDILKALTNRSGEEHAYSRRPLKR 1604
            SDG+LP Y V+ +P D ALLEL+APVHL  PK LLQ DI   L +R  EEH YSRR L R
Sbjct:  205 SDGHLPSYRVAHDPSDPALLELDAPVHLVFPKLLLQPDIKDILEDRVTEEHVYSRRRLSR 264
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BLAST of SMED30032726 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1)

HSP 1 Score: 156.377 bits (394), Expect = 5.748e-43
Identity = 79/121 (65.29%), Postives = 94/121 (77.69%), Query Frame = 2 
Query: 1064 YLIVTENSNTRWTDDDQTTLIIPNKFAGRHRQALWDWGYFLSTHRTPEWSYRNSN*CDEDVELPSPVIKRESESNLAREMRHEAEVAIQQFEHLKRKYRWKANFQGRRLAKINKYIASGRI 1426
            Y  V  NS T+W DD++TTLIIP+KFAGR+RQALWD  Y LST+ T EW  R+    DEDVELPS  IKRE   N AR++RHEAEVA+QQF+HL+RKYRWKA+ Q +RL +INK IASGRI
Sbjct:   50 YPSVIGNSGTQWKDDERTTLIIPSKFAGRYRQALWDGVYSLSTYGTSEWPNRSRIRHDEDVELPSLAIKREPGRNTARKIRHEAEVALQQFDHLERKYRWKASLQRKRLMRINKDIASGRI 170

HSP 2 Score: 109.768 bits (273), Expect = 3.038e-26
Identity = 49/81 (60.49%), Postives = 67/81 (82.72%), Query Frame = 3 
Query: 1395 KSTSTLPVVESDGYLPEYNVSFNPEDQALLELNAPVHLALPKCLLQLDILKALTNRSGEEHAYSRRPLKRGVPQGIYGHRI 1637
            K  ++  +  SDGYLP+YN++F+PED ALLEL+APVH+ALPK ++Q DIL+AL +R+ EEHAYS+RPLKR +P+  +GHRI
Sbjct:  163 KDIASGRISSSDGYLPDYNIAFDPEDPALLELSAPVHMALPKHIMQRDILEALDDRTSEEHAYSQRPLKREMPRRKFGHRI 243
[Close]
BLAST of SMED30032726 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1)

HSP 1 Score: 154.066 bits (388), Expect = 3.874e-42
Identity = 77/115 (66.96%), Postives = 92/115 (80.00%), Query Frame = 2 
Query: 1082 NSNTRWTDDDQTTLIIPNKFAGRHRQALWDWGYFLSTHRTPEWSYRNSN*CDEDVELPSPVIKRESESNLAREMRHEAEVAIQQFEHLKRKYRWKANFQGRRLAKINKYIASGRI 1426
            NS T+W DD++TTLIIP+KFAGR+RQALWD  Y LST+ T EW  R+    DEDVELPS  IKRE   N AR++RHEAEVA+QQF+HL+RKYRWKA+ Q +RL +INK IASGRI
Sbjct:   54 NSGTQWKDDERTTLIIPSKFAGRYRQALWDGVYSLSTYGTSEWPNRSRIRHDEDVELPSLAIKREPGRNTARKIRHEAEVALQQFDHLERKYRWKASLQRKRLMRINKDIASGRI 168

HSP 2 Score: 109.768 bits (273), Expect = 2.639e-26
Identity = 49/81 (60.49%), Postives = 67/81 (82.72%), Query Frame = 3 
Query: 1395 KSTSTLPVVESDGYLPEYNVSFNPEDQALLELNAPVHLALPKCLLQLDILKALTNRSGEEHAYSRRPLKRGVPQGIYGHRI 1637
            K  ++  +  SDGYLP+YN++F+PED ALLEL+APVH+ALPK ++Q DIL+AL +R+ EEHAYS+RPLKR +P+  +GHRI
Sbjct:  161 KDIASGRISSSDGYLPDYNIAFDPEDPALLELSAPVHMALPKHIMQRDILEALDDRTSEEHAYSQRPLKREMPRRKFGHRI 241
[Close]
BLAST of SMED30032726 vs. Planmine SMEST
Match: SMESG000060519.1 (SMESG000060519.1)

HSP 1 Score: 105.531 bits (262), Expect = 1.135e-38
Identity = 59/114 (51.75%), Postives = 75/114 (65.79%), Query Frame = 2 
Query: 1085 SNTRWTDDDQTTLIIPNKFAGRHRQALWDWGYFLSTHRTPEWSYRNSN*CDEDVELPSPVIKRESESNLAREMRHEAEVAIQQFEHLKRKYRWKANFQGRRLAKINKYIASGRI 1426
            S+++W D ++TTL + N+FAGR+ QALWD GY +ST+ T EW  RN    D+D ELP  +IKRE   N ARE+R +AE A+  FE LKR YR   N Q   LA+I   IAS RI
Sbjct:  851 SSSKWVDVERTTLTVQNRFAGRYHQALWDPGYSISTYGTLEWPCRNPESRDKDTELPCILIKREPGRNPAREIRQKAEGALHHFEKLKRWYRPLTNQQREHLARIIMDIASWRI 964

HSP 2 Score: 74.3294 bits (181), Expect = 1.135e-38
Identity = 35/62 (56.45%), Postives = 42/62 (67.74%), Query Frame = 3 
Query: 1428 DGYLPEYNVSFNPEDQALLELNAPVHLALPKCLLQLDILKALTNRSGEEHAYSRRPLKRGVP 1613
            DG+LP Y V++NP+D  LLE + PVHL +PK LLQ DI   L +R  EEHAYSRR L    P
Sbjct:  968 DGHLPSYGVAYNPDDPVLLESDTPVHLVVPKSLLQPDIRDILEDRVTEEHAYSRRRLSGKRP 1029
The following BLAST results are available for this feature:
BLAST of SMED30032726 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 SMED30032726 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 SMED30032726 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 SMED30032726 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 SMED30032726 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 SMED30032726 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 SMED30032726 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 SMED30032726 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 SMED30032726 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 SMED30032726 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 SMED30032726 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 SMED30032726 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 SMED30032726 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 SMED30032726 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000059844.13.486e-6366.96SMESG000059844.1[more]
SMESG000008335.17.022e-4758.56SMESG000008335.1[more]
SMESG000010307.15.748e-4365.29SMESG000010307.1[more]
SMESG000010307.13.874e-4266.96SMESG000010307.1[more]
SMESG000060519.11.135e-3851.75SMESG000060519.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032726 ID=SMED30032726|Name=SMED30032726|organism=Schmidtea mediterranea sexual|type=transcript|length=1655bp
GAAGCAGATGACTGGCAATGCACACCCGTGTTCCACTCGGAAAATCTGAC
AAAAAACGTGGTTATTAAAATGTCCACAAATATGAAGCACTAGCAGAGAA
GAAAATTTGAAGAATGGCATGTGTACCAAAAATAACTGCTACCGAAAATT
CTCGTGACTACCCAGATCACGAGCGGCATGAATCACCTCAACCGTATAAA
AAGCCTGTCGATGGATACGTGTTGTCATTATTCTACAAAAGTCATGCAAA
ATTCAAATCAAACCAAGAAACGCGATATGATTTACCACGAGTCCAGTTCA
ATGAAGAGAGAGGAAGCACGATTCACGCCGGAAGATCATGTATCGGGTGA
GGCATTTCATTTCTGAAAATCTAAATTTTTAATTTAACAAGATAATTTTA
ATCAATAATATATATTATGCCTTAGTTTCTTTTAATTTGGTTGTTCTTAA
AATTTTGTTGTATAGTATTAATAATGTAAACTGATTTTAATTTTTCTTTA
ATTTATTTTGTCGTCTGAATTTAAGTAACTTGGTTCTGATTTACAGGTAA
TAGTAACCATAAGTATCAAATATGTAGGATAATTGTAGCTTATATTAGTA
TTACAGTAGATGGATGCGGCCGTAAGTGGATAATATTTACGTTTAATTGG
ATGTATTCTCATTTTCGCCGTTCCATTAACCAATGCGTATGATTTGTTTT
ATCAAATTTATTGGCAGAGAACCGAGGACATTTTTTCGTTTCTAACCGGT
ACAAGTAGCCTTAGTCGTCCTGATTGTTATACATAAAAGAGAAACGTGGT
TGGCCATTCGGGAAAATGGACACGGTCGAGTCAAGAAGGAAGATTTAGCA
GATGTTCGACTTGTAATGAATTAAGCTGTCCAGAACGCTCAAACCAAAAA
TAAGCAAAACGCAAATTGATGCTATAGGTTGCTTATGAATAAAGTAAACT
TCGGTCCTGTGAACTTCAGGTATAGTTCCAATTACGAGAAAAATAAATTT
TTATAATTAATAAACGAATTTCTGAATATGTAACGCACGATATTGGAACT
AATTTTTTTATGATATTTAATAGTAACAGAAAATTCTAATACCCGTTGGA
CGGACGACGACCAAACTACGTTGATCATCCCAAACAAATTCGCTGGGCGC
CACCGACAGGCTCTGTGGGATTGGGGATACTTCTTATCCACGCATAGGAC
ACCAGAGTGGTCATACAGAAATAGCAACTGATGTGACGAGGACGTGGAGC
TACCCAGTCCCGTCATAAAAAGAGAGTCAGAGAGCAATCTAGCTCGGGAG
ATGCGACATGAAGCCGAGGTGGCCATCCAACAGTTCGAGCACCTCAAACG
GAAGTATCGCTGGAAGGCCAACTTCCAGGGCAGACGGTTGGCAAAAATCA
ACAAGTACATTGCCAGTGGTCGAATCCGATGGCTACTTGCCAGAATATAA
TGTGTCATTTAATCCAGAAGATCAGGCCCTCCTGGAGCTAAATGCACCGG
TACACCTAGCACTCCCAAAATGTCTCCTACAACTCGACATCCTGAAGGCG
CTAACTAACAGGTCGGGCGAGGAACACGCCTACTCGCGACGCCCTCTGAA
GCGTGGAGTCCCACAAGGAATTTATGGGCACAGAATCACGAAGTAAAACT
GTACA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..29