SMED30025148

Overview
NameSMED30025148
Smed IDSMED30025148
Length (bp)849
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 SMED30025148 (SMED30025148) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30025148 (SMED30025148) 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 SMED30025148 (SMED30025148) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30025148 (SMED30025148) 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




SMED30025148

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



PAGE Curations: 25

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30025148h1SMcG0016271 SmedASXL_016347SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
head regionSMED30025148h1SMcG0016271 SmedASXL_000713SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
head regionSMED30025148h1SMcG0016271 SmedASXL_016348SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30025148h1SMcG0016271 Contig35228newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025148h1SMcG0016271 Contig35228uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30025148h1SMcG0016271 dd_Smed_v4_1312_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30025148h1SMcG0016271 dd_Smed_v4_1312_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30025148h1SMcG0016271 dd_Smed_v4_1312_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
cilated neuronSMED30025148h1SMcG0016271 dd_Smed_v4_1312_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30025148h1SMcG0016271 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30025148h1SMcG0016271 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30025148h1SMcG0016271 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30025148h1SMcG0016271 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30025148h1SMcG0016271 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
cilated neuronSMED30025148h1SMcG0016271 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30025148h1SMcG0016271 dd_Smed_v6_4311_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30025148h1SMcG0016271 dd_Smed_v6_1312_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
whole organismSMED30025148h1SMcG0016271 Contig45580newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30025148h1SMcG0016271 Contig45580uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30025148h1SMcG0016271 Contig43299newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30025148h1SMcG0016271 Contig43299uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30025148h1SMcG0016271 dd_Smed_v4_13007_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
non-ciliated epidermisSMED30025148h1SMcG0016271 dd_Smed_v4_13007_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30025148h1SMcG0016271 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30025148h1SMcG0016271 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30025148 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001934:18537..30961 +4006
Homology
BLAST of SMED30025148 vs. Planmine SMEST
Match: SMESG000067876.1 (SMESG000067876.1)

HSP 1 Score: 60.077 bits (144), Expect = 9.542e-11
Identity = 27/69 (39.13%), Postives = 46/69 (66.67%), Query Frame = 2
Query:  122 LVTNAPAKSGEYESKVQIRCKFTNEKFQPEYRDSTSTIYMTYVNQLFLILEAQLLKSLMRLIKIIVISL 328
            +VT  PA  GE++S+V++ C +T+EK+   Y++  S  Y  + N++F  ++  LL+ L+RLI+II  SL
Sbjct:  840 IVTEKPAAPGEFQSQVEMGCSYTSEKYNSNYKNKDSDDYKVFTNKIFTSMKISLLQKLLRLIEIIFHSL 908          

HSP 2 Score: 24.6386 bits (52), Expect = 9.542e-11
Identity = 16/40 (40.00%), Postives = 21/40 (52.50%), Query Frame = 1
Query:  340 LREGSVQAQLEMVMASDTAVSSNQLLNVVTVAINTAYNGS 459
            L EGSV A +  VMAS + +  + L  +V  A   A N S
Sbjct:  908 LDEGSVVANMTFVMASASPLVGSNLSALVIAAAVDASNNS 947          
BLAST of SMED30025148 vs. Planmine SMEST
Match: SMESG000067876.1 (SMESG000067876.1)

HSP 1 Score: 60.077 bits (144), Expect = 9.940e-11
Identity = 27/69 (39.13%), Postives = 46/69 (66.67%), Query Frame = 2
Query:  122 LVTNAPAKSGEYESKVQIRCKFTNEKFQPEYRDSTSTIYMTYVNQLFLILEAQLLKSLMRLIKIIVISL 328
            +VT  PA  GE++S+V++ C +T+EK+   Y++  S  Y  + N++F  ++  LL+ L+RLI+II  SL
Sbjct:  831 IVTEKPAAPGEFQSQVEMGCSYTSEKYNSNYKNKDSDDYKVFTNKIFTSMKISLLQKLLRLIEIIFHSL 899          

HSP 2 Score: 24.6386 bits (52), Expect = 9.940e-11
Identity = 16/40 (40.00%), Postives = 21/40 (52.50%), Query Frame = 1
Query:  340 LREGSVQAQLEMVMASDTAVSSNQLLNVVTVAINTAYNGS 459
            L EGSV A +  VMAS + +  + L  +V  A   A N S
Sbjct:  899 LDEGSVVANMTFVMASASPLVGSNLSALVIAAAVDASNNS 938          
BLAST of SMED30025148 vs. Planmine SMEST
Match: SMESG000067876.1 (SMESG000067876.1)

HSP 1 Score: 59.6918 bits (143), Expect = 1.060e-10
Identity = 27/69 (39.13%), Postives = 46/69 (66.67%), Query Frame = 2
Query:  122 LVTNAPAKSGEYESKVQIRCKFTNEKFQPEYRDSTSTIYMTYVNQLFLILEAQLLKSLMRLIKIIVISL 328
            +VT  PA  GE++S+V++ C +T+EK+   Y++  S  Y  + N++F  ++  LL+ L+RLI+II  SL
Sbjct:  864 IVTEKPAAPGEFQSQVEMGCSYTSEKYNSNYKNKDSDDYKVFTNKIFTSMKISLLQKLLRLIEIIFHSL 932          

HSP 2 Score: 24.6386 bits (52), Expect = 1.060e-10
Identity = 16/40 (40.00%), Postives = 21/40 (52.50%), Query Frame = 1
Query:  340 LREGSVQAQLEMVMASDTAVSSNQLLNVVTVAINTAYNGS 459
            L EGSV A +  VMAS + +  + L  +V  A   A N S
Sbjct:  932 LDEGSVVANMTFVMASASPLVGSNLSALVIAAAVDASNNS 971          
BLAST of SMED30025148 vs. Planmine SMEST
Match: SMESG000067876.1 (SMESG000067876.1)

HSP 1 Score: 59.6918 bits (143), Expect = 1.104e-10
Identity = 27/69 (39.13%), Postives = 46/69 (66.67%), Query Frame = 2
Query:  122 LVTNAPAKSGEYESKVQIRCKFTNEKFQPEYRDSTSTIYMTYVNQLFLILEAQLLKSLMRLIKIIVISL 328
            +VT  PA  GE++S+V++ C +T+EK+   Y++  S  Y  + N++F  ++  LL+ L+RLI+II  SL
Sbjct:  855 IVTEKPAAPGEFQSQVEMGCSYTSEKYNSNYKNKDSDDYKVFTNKIFTSMKISLLQKLLRLIEIIFHSL 923          

HSP 2 Score: 24.6386 bits (52), Expect = 1.104e-10
Identity = 16/40 (40.00%), Postives = 21/40 (52.50%), Query Frame = 1
Query:  340 LREGSVQAQLEMVMASDTAVSSNQLLNVVTVAINTAYNGS 459
            L EGSV A +  VMAS + +  + L  +V  A   A N S
Sbjct:  923 LDEGSVVANMTFVMASASPLVGSNLSALVIAAAVDASNNS 962          
BLAST of SMED30025148 vs. Planmine SMEST
Match: SMESG000067876.1 (SMESG000067876.1)

HSP 1 Score: 60.077 bits (144), Expect = 1.289e-10
Identity = 27/69 (39.13%), Postives = 46/69 (66.67%), Query Frame = 2
Query:  122 LVTNAPAKSGEYESKVQIRCKFTNEKFQPEYRDSTSTIYMTYVNQLFLILEAQLLKSLMRLIKIIVISL 328
            +VT  PA  GE++S+V++ C +T+EK+   Y++  S  Y  + N++F  ++  LL+ L+RLI+II  SL
Sbjct:  838 IVTEKPAAPGEFQSQVEMGCSYTSEKYNSNYKNKDSDDYKVFTNKIFTSMKISLLQKLLRLIEIIFHSL 906          

HSP 2 Score: 24.2534 bits (51), Expect = 1.289e-10
Identity = 16/40 (40.00%), Postives = 21/40 (52.50%), Query Frame = 1
Query:  340 LREGSVQAQLEMVMASDTAVSSNQLLNVVTVAINTAYNGS 459
            L EGSV A +  VMAS + +  + L  +V  A   A N S
Sbjct:  906 LDEGSVVANMTFVMASASPLVGSNLSALVIAAAVDASNNS 945          
The following BLAST results are available for this feature:
BLAST of SMED30025148 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 SMED30025148 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 SMED30025148 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 SMED30025148 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 SMED30025148 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 SMED30025148 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 SMED30025148 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 SMED30025148 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 SMED30025148 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 SMED30025148 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 SMED30025148 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 SMED30025148 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 SMED30025148 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 SMED30025148 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000067876.19.542e-1139.13SMESG000067876.1[more]
SMESG000067876.19.940e-1139.13SMESG000067876.1[more]
SMESG000067876.11.060e-1039.13SMESG000067876.1[more]
SMESG000067876.11.104e-1039.13SMESG000067876.1[more]
SMESG000067876.11.289e-1039.13SMESG000067876.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025148 ID=SMED30025148|Name=SMED30025148|organism=Schmidtea mediterranea sexual|type=transcript|length=849bp
CACCTCCTCGACTTCAGTATCAACTAGCACTTCATCCCAATCCGTTAATA
TCACAACAACAACAGCAGCTGCCGCCAGTCCTACTGCAACAAGGTTTACG
ACAACTGTGCCAAGCAAACAATTGGTAACCAACGCCCCAGCAAAGTCAGG
AGAGTATGAGAGTAAGGTGCAAATTAGATGCAAATTCACTAACGAGAAGT
TCCAACCCGAATATAGAGATTCAACGTCGACAATCTATATGACATACGTA
AATCAGTTATTTCTAATTTTAGAAGCCCAATTGTTGAAATCTTTGATGCG
TTTAATAAAAATCATCGTCATAAGTCTGATATGTTTTTATTAAGAGAAGG
AAGTGTTCAGGCCCAATTGGAGATGGTCATGGCTTCGGATACCGCAGTTA
GTTCAAACCAGCTGCTTAACGTGGTGACAGTGGCCATTAATACCGCATAT
AACGGATCTGTAACGGGGGTCACTGTCACCGTGACTCAAACACCAACTAA
GGTCACGGATTCATCAGTTCCTGGATGGGGAATAGCCCTAATTGTTATTG
GGTCAATTATTGTTGTTGTTGCCATTCTTCTCGGGGCCTATTTTGGAGTG
AAACACGCGAATAATGTCAAAAATAGAGTGAGTGAAGATATGGAAAATCG
TAATCCAGTGGAGGGTAACGAGAATGCTGAGCATTATTCCCTAAAAAGAT
CCGGGCCTGATTATTTTACTTTGGCAGATGTCTAGATAAACTTTATTTAT
TTTTATAAATTTTCTTCTTGAAACTATTTTGAACACTCAACTGAGATTAA
TCTTCTATTTCATTTATATTAATGTGATATTTTATTAAATACTTTAATG
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protein sequence of SMED30025148-orf-1

>SMED30025148-orf-1 ID=SMED30025148-orf-1|Name=SMED30025148-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=135bp
MFLLREGSVQAQLEMVMASDTAVSSNQLLNVVTVAINTAYNGSVTGVTVT
VTQTPTKVTDSSVPGWGIALIVIGSIIVVVAILLGAYFGVKHANNVKNRV
SEDMENRNPVEGNENAEHYSLKRSGPDYFTLADV*
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protein sequence of SMED30025148-orf-2

>SMED30025148-orf-2 ID=SMED30025148-orf-2|Name=SMED30025148-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp
TSSTSVSTSTSSQSVNITTTTAAAASPTATRFTTTVPSKQLVTNAPAKSG
EYESKVQIRCKFTNEKFQPEYRDSTSTIYMTYVNQLFLILEAQLLKSLMR
LIKIIVISLICFY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000136whole organism
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 68..90