SMED30035591

Overview
NameSMED30035591
Smed IDSMED30035591
Length (bp)2563
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 SMED30035591 (SMED30035591) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035591 (SMED30035591) 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 SMED30035591 (SMED30035591) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035591 (SMED30035591) 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



SMED30035591

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30035591SMESG000079666.1 dd_Smed_v4_18061_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035591SMESG000079666.1 dd_Smed_v4_18061_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30035591SMESG000006930.1 SMESG000001565.1 Contig31198newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30035591SMESG000006930.1 SMESG000001565.1 Contig31198uc_Smed_v2PMID: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
SMED30035591 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001409:51742..54041 +9577
Homology
[Close]
BLAST of SMED30035591 vs. Planmine SMEST
Match: SMESG000063572.1 (SMESG000063572.1)

HSP 1 Score: 115.931 bits (289), Expect = 1.446e-41
Identity = 53/65 (81.54%), Postives = 56/65 (86.15%), Query Frame = 3 
Query: 1992 EKFSMQCQVAPGLKQVQYSWYHDNQLMENNQQTITFDSFTRSKFGEYKCKFVGLNQINQKVEFNG 2186
            EKFSM+CQVAP LKQVQYSWYHDNQL+ENN QTITFDSFTRSK G YKCK VGL+Q NQKVE   
Sbjct:  313 EKFSMRCQVAPELKQVQYSWYHDNQLLENNHQTITFDSFTRSKLGVYKCKIVGLDQRNQKVELEA 377

HSP 2 Score: 70.4774 bits (171), Expect = 1.446e-41
Identity = 36/47 (76.60%), Postives = 40/47 (85.11%), Query Frame = 2 
Query: 2180 QRLSYFVPIIVKLIEGAGSHVAVIMSQKKELLHEISVDSEYFGSDVR 2320
            QRLS+FVPI V+LIEGAGS VAVIMS+KKEL  EIS DSE  GSDV+
Sbjct:  381 QRLSFFVPIKVELIEGAGSQVAVIMSRKKELHCEISADSENSGSDVQ 427

HSP 3 Score: 24.6386 bits (52), Expect = 1.446e-41
Identity = 11/14 (78.57%), Postives = 12/14 (85.71%), Query Frame = 1 
Query: 2323 KFQNQELSIQDLLS 2364
            KFQNQELS QD L+
Sbjct:  429 KFQNQELSTQDSLN 442
[Close]
BLAST of SMED30035591 vs. Planmine SMEST
Match: SMESG000026481.1 (SMESG000026481.1)

HSP 1 Score: 111.694 bits (278), Expect = 2.802e-40
Identity = 51/65 (78.46%), Postives = 55/65 (84.62%), Query Frame = 3 
Query: 1992 EKFSMQCQVAPGLKQVQYSWYHDNQLMENNQQTITFDSFTRSKFGEYKCKFVGLNQINQKVEFNG 2186
            EKFSM+CQV P LKQVQYSWYHDNQL+EN QQTITF+SFTRSK G YKCK VGL+Q NQKVE   
Sbjct: 1038 EKFSMRCQVGPELKQVQYSWYHDNQLLENQQQTITFNSFTRSKLGVYKCKIVGLDQNNQKVELEA 1102

HSP 2 Score: 72.0182 bits (175), Expect = 2.802e-40
Identity = 36/47 (76.60%), Postives = 41/47 (87.23%), Query Frame = 2 
Query: 2180 QRLSYFVPIIVKLIEGAGSHVAVIMSQKKELLHEISVDSEYFGSDVR 2320
            QRLS+FVPI V+LIEGAGS VAVI+S+KKEL  EIS DSEY GSDV+
Sbjct: 1106 QRLSFFVPIKVELIEGAGSQVAVIVSRKKELHCEISADSEYSGSDVQ 1152

HSP 3 Score: 23.0978 bits (48), Expect = 2.802e-40
Identity = 10/14 (71.43%), Postives = 12/14 (85.71%), Query Frame = 1 
Query: 2323 KFQNQELSIQDLLS 2364
            KF+NQELS QD L+
Sbjct: 1154 KFENQELSTQDSLN 1167
[Close]
BLAST of SMED30035591 vs. Planmine SMEST
Match: SMESG000026481.1 (SMESG000026481.1)

HSP 1 Score: 110.923 bits (276), Expect = 3.792e-40
Identity = 51/65 (78.46%), Postives = 55/65 (84.62%), Query Frame = 3 
Query: 1992 EKFSMQCQVAPGLKQVQYSWYHDNQLMENNQQTITFDSFTRSKFGEYKCKFVGLNQINQKVEFNG 2186
            EKFSM+CQV P LKQVQYSWYHDNQL+EN QQTITF+SFTRSK G YKCK VGL+Q NQKVE   
Sbjct:  520 EKFSMRCQVGPELKQVQYSWYHDNQLLENQQQTITFNSFTRSKLGVYKCKIVGLDQNNQKVELEA 584

HSP 2 Score: 72.0182 bits (175), Expect = 3.792e-40
Identity = 36/47 (76.60%), Postives = 41/47 (87.23%), Query Frame = 2 
Query: 2180 QRLSYFVPIIVKLIEGAGSHVAVIMSQKKELLHEISVDSEYFGSDVR 2320
            QRLS+FVPI V+LIEGAGS VAVI+S+KKEL  EIS DSEY GSDV+
Sbjct:  588 QRLSFFVPIKVELIEGAGSQVAVIVSRKKELHCEISADSEYSGSDVQ 634

HSP 3 Score: 23.0978 bits (48), Expect = 3.792e-40
Identity = 10/14 (71.43%), Postives = 12/14 (85.71%), Query Frame = 1 
Query: 2323 KFQNQELSIQDLLS 2364
            KF+NQELS QD L+
Sbjct:  636 KFENQELSTQDSLN 649
[Close]
BLAST of SMED30035591 vs. Planmine SMEST
Match: SMESG000079666.1 (SMESG000079666.1)

HSP 1 Score: 80.4925 bits (197), Expect = 1.771e-18
Identity = 44/61 (72.13%), Postives = 47/61 (77.05%), Query Frame = 3 
Query:    3 MSNILSIDPKFKRNRIIDKHRLSIIAPDNLLQIWTLVRRFSNLRGNQSYQMSSLTRKCCAS 185
            MSNILSIDPKF+RNRIIDKHRLSIIAPDNLLQIWT VRR   L G  S + +   R C AS
Sbjct:    1 MSNILSIDPKFERNRIIDKHRLSIIAPDNLLQIWTFVRR--KLIGADSSEETKAIR-CQAS 58
[Close]
BLAST of SMED30035591 vs. Planmine SMEST
Match: SMESG000079666.1 (SMESG000079666.1)

HSP 1 Score: 80.4925 bits (197), Expect = 2.465e-18
Identity = 44/61 (72.13%), Postives = 47/61 (77.05%), Query Frame = 3 
Query:    3 MSNILSIDPKFKRNRIIDKHRLSIIAPDNLLQIWTLVRRFSNLRGNQSYQMSSLTRKCCAS 185
            MSNILSIDPKF+RNRIIDKHRLSIIAPDNLLQIWT VRR   L G  S + +   R C AS
Sbjct:    1 MSNILSIDPKFERNRIIDKHRLSIIAPDNLLQIWTFVRR--KLIGADSSEETKAIR-CQAS 58

HSP 2 Score: 45.0542 bits (105), Expect = 6.190e-6
Identity = 26/46 (56.52%), Postives = 26/46 (56.52%), Query Frame = 1 
Query:  118 GFPICEETKAIRCQASQENVARLI*LVGILLNCP*ELYLNLDPRVQ 255
            G    EETKAIRCQASQEN                ELYLNLDPRVQ
Sbjct:   43 GADSSEETKAIRCQASQEN----------------ELYLNLDPRVQ 72
The following BLAST results are available for this feature:
BLAST of SMED30035591 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 SMED30035591 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 SMED30035591 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 SMED30035591 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 SMED30035591 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 SMED30035591 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 SMED30035591 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 SMED30035591 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 SMED30035591 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 SMED30035591 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 SMED30035591 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 SMED30035591 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 SMED30035591 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 SMED30035591 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000063572.11.446e-4181.54SMESG000063572.1[more]
SMESG000026481.12.802e-4078.46SMESG000026481.1[more]
SMESG000026481.13.792e-4078.46SMESG000026481.1[more]
SMESG000079666.11.771e-1872.13SMESG000079666.1[more]
SMESG000079666.12.465e-1872.13SMESG000079666.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035591 ID=SMED30035591|Name=SMED30035591|organism=Schmidtea mediterranea sexual|type=transcript|length=2563bp
AAATGTCTAACATTCTCTCAATAGATCCAAAGTTCAAGCGTAACCGAATT
ATCGATAAGCACCGTTTATCAATAATTGCACCTGACAATTTGCTTCAAAT
CTGGACTTTGGTACGAAGGTTTTCCAATTTGCGAGGAAACCAAAGCTATC
AGATGTCAAGCCTCACAAGAAAATGTTGCGCGTCTTATCTAACTTGTTGG
AATATTATTAAATTGTCCATAGGAATTATATCTCAATCTGGATCCTCGTG
TTCAATGAAAAATAAACAATATTCGAATCCCAACAAAATAATTTTTATTT
AATTACAATCGAATTCACTCGTTTCAAACATTTAGTGGACGCTTAATGGA
TCTCGACATAGAATTTCTTTTGGATAATGCTCTTTTCAATTTGTCCATAT
CAGTGGCCAAAAAGCTTCATCAGCAGATTGATCTGCTCAAGGACCGATGT
AATCAGGAGCTCAGACAGAAATTCACTGATTACTACAGAAGGTTTCGTGT
CCTTATCATCCTAAGGTCCCCCGTTTCGATCAATACTAAATGAATCAAGT
AACAATTTATTCACCAAAAATGAAATCAAAAAACATCGAAATAGCAATTA
TTGTAATTCAAATAGTTCCGAGGTCTTCTTTAATTGACCTAATGAACGAG
ATACTTTTAATTTTCAATTTCGAGCCGTTTCATGGTTTCCAGGAAAAGGT
TTGAAGGGTGGAGGTATTCTTCTGATGGTAATAGCCAAATAATTTACTTC
GTGGGATGCCATAGGCTGGGAGTTCTAGTAATCTCGGCGGAATGGGCATA
GTGGGCAAGGAACAACTCTGATTCAGAATATTTCGACTGGACATTTAAAT
CATTTAGAATGTGGCACTGTGCTTCTAATTTCTAGATAATGTTTGACAGC
TCCCGTATTTAACCTTTAATGCCCTCGATATGTTCATCTATTCATTTTAT
TGACTCTTGGGCAGATCAATCTGCTGACGGAGTTTCTTGCCGCCGCCTCT
AAACGGATCCAAGTTTGCTCCATGCGCTGACAGCGGCGTACCATAGATTC
TGCAAACGGCGATTGCTTCATCACCTCGTCATGATATTTTGAAACATCTC
ACCGATATTTATCAAATTTTTTAAAAATCGAATAATTTTTCTTAAATTAA
TTGATTTAAGTTGGTATTGATTTATTATTAATTCACTGTGTTATATTGAT
ATTCGAGTGTAGGGAGTTGATTAGAGACCATGAAAAATAAGTTTCGTTAA
GATTTTAGTAAAAAATGGTTTTGAGCTCTTTCTCGTAAAAATATTTATAA
ATTTTTGATTATTAAATGCCAATGCAACATTTAATAGTAGTAAAAGGCGA
TCAAAGTCACAACGACAATTTCCAAACACGTCTCTACTCCAATTGACATA
CGGATGATATTGCCGACGGAACAAAAAGGCCTCAAAATAGAATTCCATTC
GGAAAACTTTACCAAAATTACTATAGAGTTCTTAGTCAAGTGGGAGAACT
GATTAAAGATGATGAAAACAATCATAAGACGAGTATCAACGAAGCATTTC
AAGATGTACATTATGACGATTATTAATTCCTTTTAATATAATCACATATT
TATTAAAATCCGCGCACATGTTTATATTAGTTGGCGAGTCACTATTTTGT
AAATCAAATTTTTGGAATGTTCTAAGGTTGTTTTATTGTGTATGAGCTTA
CGTTCAAACGTTTTGTGTTAATGAATGTTTTCAAACAAGGAAAATATCAG
GTTATTCATAATTTTCATTTCGAATAATTGGATTGTTAATTAATTCATGG
AGCAAACAATTGCGAAACTATATTCATAACTATAGAGACACAATAATAAC
ATCAATAATGTATTCAATATAAATCCGATAAGCTGATTTGATCCGTTGAA
CTTTGTGTTCGATTATTGGTCAGTTGGTCACGGAGCATTCGATATCAAGG
TTTTTCGTTTCTTCAAATCTCATAGTGTTGTTAGTGGAATAGAGAAATTC
TCAATGCAATGTCAAGTGGCACCCGGATTGAAACAAGTTCAATATTCTTG
GTATCATGACAACCAACTGATGGAAAACAATCAACAAACGATAACCTTTG
ACAGTTTCACACGTTCAAAGTTTGGAGAGTATAAATGCAAATTCGTCGGA
CTGAATCAAATAAATCAGAAAGTAGAATTCAACGGCTTTCATATTTTGTA
CCTATTATAGTTAAACTAATTGAAGGAGCCGGATCACATGTTGCTGTGAT
CATGTCGCAAAAGAAAGAACTTCTTCATGAAATCTCTGTTGACAGTGAAT
ATTTTGGATCAGATGTTCGATGAAGTTCCAAAACCAAGAATTATCTATTC
AAGATTTATTATCATTTATGTTACTGATTTAAACAAATTCAAAAAAATAT
TCAACTGAAATCAAATTAATCGTTATATAATAAATCATTTTTATTTTTTG
AAAAAGATTGCCACAGCATAGACAATTTTATTTAACAATAATTTATAATT
AAATATATAATTATTTAATCAACTAATCTATATATTTAGAGAAACATCGA
GGCATTAACTGAA
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protein sequence of SMED30035591-orf-1

>SMED30035591-orf-1 ID=SMED30035591-orf-1|Name=SMED30035591-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp
MSNILSIDPKFKRNRIIDKHRLSIIAPDNLLQIWTLVRRFSNLRGNQSYQ
MSSLTRKCCASYLTCWNIIKLSIGIISQSGSSCSMKNKQYSNPNKIIFI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR013783Ig-like_fold
IPR007110Ig-like_dom
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding