SMED30011678

Overview
NameSMED30011678
Smed IDSMED30011678
Length (bp)2174
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 SMED30011678 (SMED30011678) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011678 (SMED30011678) 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 SMED30011678 (SMED30011678) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011678 (SMED30011678) 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



SMED30011678

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30011678h1SMcG0012095 SmedASXL_015885SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30011678h1SMcG0012095 SmedASXL_015885SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30011678h1SMcG0012095 Contig45356uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011678h1SMcG0012095 Contig45356newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011678h1SMcG0012095 Contig34563uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011678h1SMcG0012095 Contig34563newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
neoblastSMED30011678h1SMcG0012095 dd_Smed_v4_7612_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30011678h1SMcG0012095 dd_Smed_v6_7612_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
neuronSMED30011678h1SMcG0012095 Contig44727uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30011678h1SMcG0012095 Contig44727newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
zeta neoblastSMED30011678h1SMcG0012095 dd_Smed_v4_7612_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30011678h1SMcG0012095 SMED_05209_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011678h1SMcG0012095 SMED_05209_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011678 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000025:250463..252885 +10866
Homology
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BLAST of SMED30011678 vs. Planmine SMEST
Match: SMESG000004883.1 (SMESG000004883.1)

HSP 1 Score: 137.502 bits (345), Expect = 4.690e-36
Identity = 67/81 (82.72%), Postives = 70/81 (86.42%), Query Frame = 2 
Query:  440 ARRRLERIKAAIASGEIPSTDEYTPDYGVSFKLRDPALTRM*APTNIVLQVNLFNGPIQHRDRRDEHFYQCQRPIKKERNK 682
            ARRRLERI A IASGEIPSTD Y PDYGVSF+LRDPA  RM APTNIVL VNLFNGPI+HRDRRDEH YQCQ P KKERN+
Sbjct:    2 ARRRLERINAVIASGEIPSTDGYAPDYGVSFELRDPA--RMKAPTNIVLPVNLFNGPIRHRDRRDEHSYQCQHPTKKERNQ 80

HSP 2 Score: 67.3958 bits (163), Expect = 1.316e-24
Identity = 38/94 (40.43%), Postives = 58/94 (61.70%), Query Frame = 2 
Query:  440 ARRRLERIKAAIASGEIPSTDEYTPDYGVSFKLRDPALTRM*APTNIVLQVNLFNGPIQHR---DRRDEHFYQCQRPIKKERNKCMQSLQNQRF 712
            AR+RL ++   IASG IPSTD + P+YGVSF+L DP LT+M APT +V+   L    +++R    +  +H Y  + P   + N    +L+++RF
Sbjct:  181 ARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVRSTLRNRLGSSQTGDHTYASRHP---QWNSKHNNLRSERF 271

HSP 3 Score: 47.7506 bits (112), Expect = 1.316e-24
Identity = 23/44 (52.27%), Postives = 31/44 (70.45%), Query Frame = 3 
Query:  303 DDI*VLSLTIKREPGRNSAREARQRAEFLVYRLEALVRKFQWKV 434
            +++ + S+ IKREPG N AREARQRAE+   + E L RK+Q K 
Sbjct:  135 EEVELPSVAIKREPGHNPAREARQRAEYAAMKKEELERKYQRKA 178

HSP 4 Score: 38.1206 bits (87), Expect = 1.316e-24
Identity = 19/40 (47.50%), Postives = 22/40 (55.00%), Query Frame = 1 
Query:  169 SDNDWVAIRVAPDLTTHYMQSLWDVGCSLSTLEDSSWPIR 288
            SDN  V +++       Y Q LWD G  LST  DSSWP R
Sbjct:   90 SDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRR 129
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BLAST of SMED30011678 vs. Planmine SMEST
Match: SMESG000046320.1 (SMESG000046320.1)

HSP 1 Score: 130.183 bits (326), Expect = 9.441e-35
Identity = 62/119 (52.10%), Postives = 83/119 (69.75%), Query Frame = 3 
Query: 1029 LIMLQFTNTFTSGMDAIHVINQELSRLREAKLDIHHHLSQVSKECQEIKSTWVKPERAKNVYHKINAAQNGWQEERQLVQALRTQIRGLEVALTSNQEGNAVTYPLVFFPA*LVYCDHG 1385
            L+ +QF  T    MD I ++  EL+R ++A  D+H  L  + +E Q++K+TWV P R K +Y K+ AAQ GW EERQLV +L+TQIRGLEVAL+++QEG AVTYPLVF PA L Y +  
Sbjct:    8 LVAIQFIRTILE-MDPIKLLQNELTRTQQANNDLHDQLLHLVREMQQLKATWVNPTRVKPLYQKLAAAQKGWAEERQLVTSLKTQIRGLEVALSASQEGAAVTYPLVFAPAQLAYRESS 125
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BLAST of SMED30011678 vs. Planmine SMEST
Match: SMESG000049741.1 (SMESG000049741.1)

HSP 1 Score: 127.872 bits (320), Expect = 6.591e-34
Identity = 61/115 (53.04%), Postives = 82/115 (71.30%), Query Frame = 3 
Query: 1029 LIMLQFTNTFTSGMDAIHVINQELSRLREAKLDIHHHLSQVSKECQEIKSTWVKPERAKNVYHKINAAQNGWQEERQLVQALRTQIRGLEVALTSNQEGNAVTYPLVFFPA*LVY 1373
            L+ +QF  T    MD I ++  EL+R ++A  D+H  L  + +E Q++K+TWV P + K +Y K+ AAQ GW EERQLV +L+TQIRGLEVAL+++QEG AVTYPLVF PA L Y
Sbjct:    8 LVAIQFIRTILD-MDPIKLLQNELTRTQQANNDLHDQLLHLVREMQQLKATWVNPTKVKPLYLKLAAAQKGWAEERQLVTSLKTQIRGLEVALSASQEGAAVTYPLVFAPAQLAY 121
[Close]
BLAST of SMED30011678 vs. Planmine SMEST
Match: SMESG000042603.1 (SMESG000042603.1)

HSP 1 Score: 125.561 bits (314), Expect = 2.266e-33
Identity = 56/102 (54.90%), Postives = 76/102 (74.51%), Query Frame = 3 
Query: 1068 MDAIHVINQELSRLREAKLDIHHHLSQVSKECQEIKSTWVKPERAKNVYHKINAAQNGWQEERQLVQALRTQIRGLEVALTSNQEGNAVTYPLVFFPA*LVY 1373
            MD   ++ QELSR ++    ++  + Q++KE Q++KSTWV P R K++Y ++ AAQ GW EERQL Q+LRTQIRGLEVAL ++QEG AVTYPL+F P+ L Y
Sbjct:    1 MDPTRLLQQELSRAQQNNQSLYGQILQLTKEVQQVKSTWVDPARLKSIYQRLTAAQRGWAEERQLNQSLRTQIRGLEVALAASQEGQAVTYPLIFAPSQLPY 102
[Close]
BLAST of SMED30011678 vs. Planmine SMEST
Match: SMESG000021315.1 (SMESG000021315.1)

HSP 1 Score: 124.79 bits (312), Expect = 4.765e-33
Identity = 56/102 (54.90%), Postives = 76/102 (74.51%), Query Frame = 3 
Query: 1068 MDAIHVINQELSRLREAKLDIHHHLSQVSKECQEIKSTWVKPERAKNVYHKINAAQNGWQEERQLVQALRTQIRGLEVALTSNQEGNAVTYPLVFFPA*LVY 1373
            MD I ++  EL+R ++A  D+H  L  + +E Q++K+TW+ P + K +Y K+ AAQ GW EERQLV +L+TQIRGLEVAL+++QEG AVTYPLVF PA L Y
Sbjct:    1 MDPIKLLQNELTRTQQANNDLHDQLLHLVREMQQLKATWINPTKVKPLYQKLAAAQKGWAEERQLVTSLKTQIRGLEVALSASQEGAAVTYPLVFAPAQLAY 102
The following BLAST results are available for this feature:
BLAST of SMED30011678 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 SMED30011678 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 SMED30011678 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 SMED30011678 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 SMED30011678 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 SMED30011678 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 SMED30011678 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 SMED30011678 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 SMED30011678 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 SMED30011678 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 SMED30011678 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 SMED30011678 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 SMED30011678 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 SMED30011678 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000004883.14.690e-3682.72SMESG000004883.1[more]
SMESG000046320.19.441e-3552.10SMESG000046320.1[more]
SMESG000049741.16.591e-3453.04SMESG000049741.1[more]
SMESG000042603.12.266e-3354.90SMESG000042603.1[more]
SMESG000021315.14.765e-3354.90SMESG000021315.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011678 ID=SMED30011678|Name=SMED30011678|organism=Schmidtea mediterranea sexual|type=transcript|length=2174bp
GTAGGAAGATAACGAACACCCAGAAAATTACATCGATGAGGAAAGCTAGA
GGTCTAGCAATGGGGAGAAATCATCGACTTGGATCCTCCACGACCTTCTG
ACCACCAGCAGGATGTTACCACGATCTTCCCCGAGAGAGATACACGTCCA
ACAGAATCTGAAATCCGGAGTGACAACGACTGGGTGGCCATTCGAGTAGC
CCCCGACCTGACAACACACTACATGCAGTCATTATGGGACGTCGGCTGCA
GCCTCTCCACGTTGGAGGATAGTAGTTGGCCCATCAGAGAAGGCTCCTGC
AGGACGATATCTAGGTACTCAGTCTCACCATCAAGCGGGAACCCGGCCGA
AATTCGGCTCGAGAAGCGCGACAGCGCGCAGAATTTTTGGTCTATAGATT
GGAAGCCTTAGTCCGAAAGTTTCAATGGAAAGTGAAGATGCAAGGAGACG
ATTGGAAAGAATCAAAGCCGCGATTGCCTCAGGCGAGATCCCCAGCACAG
ACGAATATACGCCGGACTATGGCGTCTCCTTCAAGTTGAGAGATCCAGCA
CTCACACGGATGTGAGCACCCACAAACATTGTCCTTCAGGTTAACTTATT
CAATGGCCCAATCCAACACCGGGACAGAAGAGATGAGCACTTCTATCAGT
GCCAACGCCCAATTAAAAAGGAACGAAATAAATGCATGCAGTCACTACAG
AACCAAAGATTTGAAGACCTTACTGAGAGTGAAATCACGAGCTATCACCA
TTCGTTGTTAAACGTTAGTAAAATTTAGTTTTTTTAAATGAACTTTTGTA
TATAATTCTTATTAAATGAAAATTTGAGGCATATCAAATGAGTTTTAATT
CAGTAGGACTTAAATTGTAAATTCCATACTTAGAATATGAATAACGAAAC
CGAAGCCTCATGTGTTAATACGACATAAAAATCCATAACTTAATAAATAT
AGTTCATAATTTTACGCAAAGTTTTTTTTAAAATTGTGATATTACCAACA
CCATAAAGAATCTTTGATTTCGTCACCACTCATCATGTTACAGTTCACTA
ATACTTTCACTTCAGGTATGGATGCCATTCACGTTATTAATCAAGAACTA
TCCCGTCTACGAGAAGCCAAACTGGATATCCACCACCACCTATCGCAAGT
CAGCAAGGAATGCCAGGAAATCAAATCGACTTGGGTCAAACCCGAGCGGG
CGAAGAATGTTTATCATAAGATAAATGCAGCTCAAAACGGCTGGCAGGAG
GAACGGCAATTGGTACAGGCATTACGTACTCAGATACGCGGACTGGAGGT
AGCGTTAACTTCTAATCAAGAGGGAAATGCAGTTACCTACCCATTGGTCT
TCTTCCCAGCTTAGTTGGTCTACTGCGATCACGGAACCAAGAATAACAGA
CCCCACTCTCGTCCAGGAAGGTCCGAACGAAGACGATGACGCCTAATTAC
AGCCAATAAGCCCCATGGAGAACAAGAACAGATCAAATGAACTAGTCGAA
TGATATGATGAATTGATGAATTGTTGCGGTGTAGAAAATAAATGTTTTAC
TAAACAATATGATAGCTATAGTTTTCTTGTTATTCATTTATTTTGCTGTA
AATAAAGAGGCTCTAGGATTCGGAGAGATGTAGGAAATATTCAATGTGAA
AGTTAGGGACGAATAAGTGTAAGTCGAGCATATACCTTCTAAGTGTAGCT
CGCTGAACCCAACTGAAGAGAGGGCCTTAGCAGTTTTAGAAACAAAGCTC
ACCTTTGGCTATCTCAGAACCATTATTTACATTACCAACGTTGCATAGCA
ACGGGTAACCAGTGGAGTCGAACGATTGTATGTCAAGGGTTCAAGGTCAG
ACAGTCCACGAACCCTACATTAATCATGACAACATGGATCACATTTCACT
GGAAACCGTCCATTGGAATATGCATCTCCAACGTCATTTATGACGGGTAT
CCAATGATCTCTTATGGACATATCTGATGGAAACCCTTTAGCAAATCTTA
TTTTATTTTTTACCACAAGTTACCCAACATTTACATTACTAAAATGGGGT
TTATGCTTTACTTACGCTTGCTATATGGTAGCTAGACCACTGATAAAAAC
CAAAAATTATTTTTATTACCATTTGAAAATGACATTAAAAATATTCTACA
AATTATTTGAAATATACAAACATA
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protein sequence of SMED30011678-orf-1

>SMED30011678-orf-1 ID=SMED30011678-orf-1|Name=SMED30011678-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=110bp
MLQFTNTFTSGMDAIHVINQELSRLREAKLDIHHHLSQVSKECQEIKSTW
VKPERAKNVYHKINAAQNGWQEERQLVQALRTQIRGLEVALTSNQEGNAV
TYPLVFFPA*
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