SMED30009381

Overview
NameSMED30009381
Smed IDSMED30009381
Length (bp)811
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 SMED30009381 (SMED30009381) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009381 (SMED30009381) 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 SMED30009381 (SMED30009381) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009381 (SMED30009381) 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




SMED30009381

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
central nervous systemSMED30009381 dd_Smed_v4_12259_2_2dd_Smed_v4PMID:27063937
Scimone et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
headSMED30009381 dd_Smed_v4_12259_2_2dd_Smed_v4PMID:27063937
Scimone et al., 2016
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30009381 dd_Smed_v4_12259_2_2dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009381 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000120:170154..170962 -3448
v31.002260:60008..60828 -3139
v31.000141:236330..237117 +2713
Homology
BLAST of SMED30009381 vs. Planmine SMEST
Match: SMESG000009301.1 (SMESG000009301.1)

HSP 1 Score: 127.487 bits (319), Expect = 2.402e-37
Identity = 59/80 (73.75%), Postives = 66/80 (82.50%), Query Frame = -1
Query:  485 WECKEVWHIRVQCPNIKCSYCKKAGYFKFQCFN----QTYRYQQNMSAISDQGDDKNMMSDSEYPKGDAPTVKEVTGTIN 712
            W CKEV HIR Q PNIKCS CKKAG+FKFQCF+    Q+YRYQQNM+AI DQGDD+NMMSDSEYP G+APT +EV G IN
Sbjct:  602 WGCKEVEHIRAQYPNIKCSQCKKAGHFKFQCFDLRGTQSYRYQQNMAAIIDQGDDENMMSDSEYPNGNAPTEEEVIGAIN 681          

HSP 2 Score: 46.595 bits (109), Expect = 2.402e-37
Identity = 23/36 (63.89%), Postives = 29/36 (80.56%), Query Frame = -3
Query:  702 RLSILPTQNKSDFSNSYKQSNRR*EQLRSKQRLGMQ 809
            R S+LP QN+SD SNSY++SN+R EQLRSKQ  G +
Sbjct:  570 RSSLLPIQNRSDISNSYERSNKRYEQLRSKQCWGCK 605          
BLAST of SMED30009381 vs. Planmine SMEST
Match: SMESG000037636.1 (SMESG000037636.1)

HSP 1 Score: 105.145 bits (261), Expect = 2.347e-31
Identity = 49/77 (63.64%), Postives = 59/77 (76.62%), Query Frame = -1
Query:  494 WECKEVWHIRVQCPNIKCSYCKKAGYFKFQCFN----QTYRYQQNMSAISDQGDDKNMMSDSEYPKGDAPTVKEVTG 712
            W  KEV HIR Q PNIKCSYCKKAG+ KF CF+    ++YRYQQNM+AI+ QGDDK MMSDS+Y   +APT +E+ G
Sbjct: 1171 WRYKEVGHIRAQYPNIKCSYCKKAGHLKFHCFDLRGTESYRYQQNMAAIAYQGDDKKMMSDSKYQNANAPTQEELLG 1247          

HSP 2 Score: 48.9062 bits (115), Expect = 2.347e-31
Identity = 24/31 (77.42%), Postives = 29/31 (93.55%), Query Frame = -3
Query:  717 RLSILPTQNKSDFSNSYKQSNRR*EQLRSKQ 809
            R S+LPTQN+S+FSNSY++SNRR EQLRSKQ
Sbjct: 1139 RPSVLPTQNRSNFSNSYERSNRRYEQLRSKQ 1169          
BLAST of SMED30009381 vs. Planmine SMEST
Match: SMESG000037636.1 (SMESG000037636.1)

HSP 1 Score: 102.064 bits (253), Expect = 1.668e-30
Identity = 48/75 (64.00%), Postives = 57/75 (76.00%), Query Frame = -1
Query:  500 WECKEVWHIRVQCPNIKCSYCKKAGYFKFQCFN----QTYRYQQNMSAISDQGDDKNMMSDSEYPKGDAPTVKEV 712
            W  KEV HIR Q PNIKCSYCKKAG+ KF CF+    ++YRYQQNM+AI+ QGDDK MMSDS+Y   +APT +E 
Sbjct: 1220 WRYKEVGHIRAQYPNIKCSYCKKAGHLKFHCFDLRGTESYRYQQNMAAIAYQGDDKKMMSDSKYQNANAPTQEET 1294          

HSP 2 Score: 48.9062 bits (115), Expect = 1.668e-30
Identity = 24/31 (77.42%), Postives = 29/31 (93.55%), Query Frame = -3
Query:  717 RLSILPTQNKSDFSNSYKQSNRR*EQLRSKQ 809
            R S+LPTQN+S+FSNSY++SNRR EQLRSKQ
Sbjct: 1188 RPSVLPTQNRSNFSNSYERSNRRYEQLRSKQ 1218          
BLAST of SMED30009381 vs. Planmine SMEST
Match: SMESG000064279.1 (SMESG000064279.1)

HSP 1 Score: 97.4413 bits (241), Expect = 1.588e-24
Identity = 50/93 (53.76%), Postives = 63/93 (67.74%), Query Frame = -1
Query:  542 DFQFYRHKTNRIFQILISSQIEDRNNYDQNKGWECKEVWHIRVQCPNIKCSYCKKAGYFKFQCFN----QTYRYQQNMSAISDQGDDKNMMSD 808
            DF     ++NR +++L S Q            W CKEV HIR Q PNIK S+CKK+G+FKFQCF+    Q+YRYQQN+ AI+DQGDD+NMMSD
Sbjct:  104 DFSNSYEQSNRRYELLRSKQ-----------RWGCKEVGHIRAQYPNIKSSHCKKSGHFKFQCFDRRGTQSYRYQQNIVAITDQGDDENMMSD 185          

HSP 2 Score: 52.7582 bits (125), Expect = 3.620e-8
Identity = 26/36 (72.22%), Postives = 30/36 (83.33%), Query Frame = -3
Query:  702 RLSILPTQNKSDFSNSYKQSNRR*EQLRSKQRLGMQ 809
            R S+LP QN+SDFSNSY+QSNRR E LRSKQR G +
Sbjct:   93 RPSVLPIQNRSDFSNSYEQSNRRYELLRSKQRWGCK 128          
BLAST of SMED30009381 vs. Planmine SMEST
Match: SMESG000037636.1 (SMESG000037636.1)

HSP 1 Score: 102.064 bits (253), Expect = 3.628e-24
Identity = 48/75 (64.00%), Postives = 57/75 (76.00%), Query Frame = -1
Query:  500 WECKEVWHIRVQCPNIKCSYCKKAGYFKFQCFN----QTYRYQQNMSAISDQGDDKNMMSDSEYPKGDAPTVKEV 712
            W  KEV HIR Q PNIKCSYCKKAG+ KF CF+    ++YRYQQNM+AI+ QGDDK MMSDS+Y   +APT +E 
Sbjct: 1189 WRYKEVGHIRAQYPNIKCSYCKKAGHLKFHCFDLRGTESYRYQQNMAAIAYQGDDKKMMSDSKYQNANAPTQEET 1263          
The following BLAST results are available for this feature:
BLAST of SMED30009381 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 SMED30009381 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 SMED30009381 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 SMED30009381 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 SMED30009381 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 SMED30009381 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 SMED30009381 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 SMED30009381 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 SMED30009381 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 SMED30009381 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 SMED30009381 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 SMED30009381 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 SMED30009381 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 SMED30009381 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000009301.12.402e-3773.75SMESG000009301.1[more]
SMESG000037636.12.347e-3163.64SMESG000037636.1[more]
SMESG000037636.11.668e-3064.00SMESG000037636.1[more]
SMESG000064279.11.588e-2453.76SMESG000064279.1[more]
SMESG000037636.13.628e-2464.00SMESG000037636.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009381 ID=SMED30009381|Name=SMED30009381|organism=Schmidtea mediterranea sexual|type=transcript|length=811bp
TCAATTCCTCCTTTTAGACTTGGTGAAATTTCATTTTCAATGAAGAAATC
AACATTATTTTCTTGATTTATAATTTTTATTTTTAACGAAACTTTGCCTA
ATATTTCTAAGAAGCTCTCATTTACACACTTTACCAATAAATTAGTATTT
TCAACTTTTACATTTTCGAGCGCGTTTATTATTTCTTTACTGATGACACT
TATTTTAGCCCCCGTATACAAAAGGCAATTAAATTTCTTATTATTGATCA
AGATACTGGGCCCACCCCTCATTCTATCATATTTTATTACACTATCATAA
CCATTATTTAAAGTGGCTAATTTATTGTTCATCCTTTTATCTATTTTACA
TACTGCATCTAGCCATAGAACATCAAGCATAACAACACCATCATACCAAA
TATTATCAAAAAATTCAATTTCATGCAAACAATTACCAACATTATCATAC
ATACATTCATTGCCCAAGATGTTACTTACATTTAGTTTATCGTTCCAGTC
ACTTCCTTTACTGTTGGAGCGTCGCCTTTTGGGTATTCGCTGTCGGACAT
CATGTTTTTATCATCTCCTTGATCTGAAATTGCTGACATATTTTGTTGAT
ATCTGTATGTTTGATTAAAGCATTGGAATTTAAAATAGCCTGCCTTCTTG
CAATAAGAACATTTTATGTTCGGACATTGGACTCTTATATGCCAAACTTC
TTTGCATTCCCAGCCTTTGTTTTGATCGTAGTTGTTCCTATCTTCTATTT
GACTGCTTATAAGAATTTGAAAAATCCGATTTGTTTTGTGTCGGTAGAAT
TGAAAGTCGAC
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protein sequence of SMED30009381-orf-1

>SMED30009381-orf-1 ID=SMED30009381-orf-1|Name=SMED30009381-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=110bp
VDFQFYRHKTNRIFQILISSQIEDRNNYDQNKGWECKEVWHIRVQCPNIK
CSYCKKAGYFKFQCFNQTYRYQQNMSAISDQGDDKNMMSDSEYPKGDAPT
VKEVTGTIN*
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protein sequence of SMED30009381-orf-2

>SMED30009381-orf-2 ID=SMED30009381-orf-2|Name=SMED30009381-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=150bp
MYDNVGNCLHEIEFFDNIWYDGVVMLDVLWLDAVCKIDKRMNNKLATLNN
GYDSVIKYDRMRGGPSILINNKKFNCLLYTGAKISVISKEIINALENVKV
ENTNLLVKCVNESFLEILGKVSLKIKIINQENNVDFFIENEISPSLKGGI
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000103central nervous system
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR021109Peptidase_aspartic_dom_sf