SMED30012398

Overview
NameSMED30012398
Smed IDSMED30012398
Length (bp)748
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 SMED30012398 (SMED30012398) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012398 (SMED30012398) 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 SMED30012398 (SMED30012398) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30012398 (SMED30012398) 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




SMED30012398

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30012398 Contig18764newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30012398 Contig18764uc_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
SMED30012398 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004537:11074..11901 +3368
v31.003322:25750..26571 -3256
v31.014254:13565..14390 -3135
v31.004288:25366..26191 +3090
v31.003631:39644..40590 -2921
v31.005844:22381..23260 +2646
v31.019216:3384..4246 -2595
v31.000350:150119..151612 -2487
Homology
BLAST of SMED30012398 vs. Planmine SMEST
Match: SMESG000042071.1 (SMESG000042071.1)

HSP 1 Score: 238.424 bits (607), Expect = 9.156e-81
Identity = 117/118 (99.15%), Postives = 117/118 (99.15%), Query Frame = 2
Query:  161 MLLKAFLFIAITVVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMRITGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNAAKNSITAKSNAPRKYKRKKCYFNFA 514
            M LKAFLFIAITVVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMRITGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNAAKNSITAKSNAPRKYKRKKCYFNFA
Sbjct:    1 MQLKAFLFIAITVVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMRITGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNAAKNSITAKSNAPRKYKRKKCYFNFA 118          
BLAST of SMED30012398 vs. Planmine SMEST
Match: SMESG000042755.1 (SMESG000042755.1)

HSP 1 Score: 231.491 bits (589), Expect = 4.006e-78
Identity = 113/118 (95.76%), Postives = 116/118 (98.31%), Query Frame = 2
Query:  161 MLLKAFLFIAITVVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMRITGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNAAKNSITAKSNAPRKYKRKKCYFNFA 514
            M LKAFLFIAIT+VNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMR++GCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNAAKNSITAKSNAPRKYKRKK YFNFA
Sbjct:    1 MQLKAFLFIAITLVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMRLSGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNAAKNSITAKSNAPRKYKRKKFYFNFA 118          
BLAST of SMED30012398 vs. Planmine SMEST
Match: SMESG000042052.1 (SMESG000042052.1)

HSP 1 Score: 200.675 bits (509), Expect = 2.498e-76
Identity = 98/110 (89.09%), Postives = 102/110 (92.73%), Query Frame = 2
Query:  161 MLLKAFLFIAITVVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMRITGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNAAKNSITAKSNAPRKYKR 490
            M LKAFLFIAITVVNIQLRTVESISCKIC+PCWNSTSDDQY DGF NGNMR++GCKSCRTNIKNNIIMKSCSEETCD KEAGEECCTEELCN+AKN  TAKSNA  KYKR
Sbjct:    1 MQLKAFLFIAITVVNIQLRTVESISCKICNPCWNSTSDDQYSDGFSNGNMRLSGCKSCRTNIKNNIIMKSCSEETCDKKEAGEECCTEELCNSAKNRKTAKSNARSKYKR 110          

HSP 2 Score: 92.8189 bits (229), Expect = 2.498e-76
Identity = 44/47 (93.62%), Postives = 44/47 (93.62%), Query Frame = 1
Query:  592 SANPFIFEQFISSFDTIQQHRVVLFNEIIHYSLFIYLYQEMKFFTNK 732
             ANPFI EQFISSFDTIQQHRVVLFNEIIHY LFIYLYQEMKFFTNK
Sbjct:  128 CANPFISEQFISSFDTIQQHRVVLFNEIIHYILFIYLYQEMKFFTNK 174          

HSP 3 Score: 32.3426 bits (72), Expect = 2.498e-76
Identity = 16/19 (84.21%), Postives = 17/19 (89.47%), Query Frame = 3
Query:  489 ERNVISILPEFNRIICSAV 545
            +RNVISIL EFN IICSAV
Sbjct:  109 KRNVISILLEFNGIICSAV 127          
BLAST of SMED30012398 vs. Planmine SMEST
Match: SMESG000042059.1 (SMESG000042059.1)

HSP 1 Score: 195.667 bits (496), Expect = 1.607e-73
Identity = 97/110 (88.18%), Postives = 100/110 (90.91%), Query Frame = 2
Query:  161 MLLKAFLFIAITVVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMRITGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNAAKNSITAKSNAPRKYKR 490
            M LKAFLFIAITVVNIQLRTVESISC IC+PCW+STSDDQY DGF N NMRITGCKSCRTNIKNNIIMKSCSEETCD KEAGEECCTEELCN+AKN  TAKSNA  KYKR
Sbjct:    1 MQLKAFLFIAITVVNIQLRTVESISCNICNPCWSSTSDDQYSDGFSNENMRITGCKSCRTNIKNNIIMKSCSEETCDKKEAGEECCTEELCNSAKNRKTAKSNARSKYKR 110          

HSP 2 Score: 88.5817 bits (218), Expect = 1.607e-73
Identity = 42/47 (89.36%), Postives = 43/47 (91.49%), Query Frame = 1
Query:  592 SANPFIFEQFISSFDTIQQHRVVLFNEIIHYSLFIYLYQEMKFFTNK 732
             ANPFI EQFISSFDTI+QHRVVLFNEIIHY LFIY YQEMKFFTNK
Sbjct:  128 CANPFISEQFISSFDTIRQHRVVLFNEIIHYILFIYFYQEMKFFTNK 174          

HSP 3 Score: 31.9574 bits (71), Expect = 1.607e-73
Identity = 16/19 (84.21%), Postives = 17/19 (89.47%), Query Frame = 3
Query:  489 ERNVISILPEFNRIICSAV 545
            +RNVISIL EFN IICSAV
Sbjct:  109 KRNVISILLEFNGIICSAV 127          
BLAST of SMED30012398 vs. Planmine SMEST
Match: SMESG000057926.1 (SMESG000057926.1)

HSP 1 Score: 103.219 bits (256), Expect = 6.432e-31
Identity = 57/100 (57.00%), Postives = 63/100 (63.00%), Query Frame = 2
Query:  191 ITVVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMRITGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNA-----AKNSITAKSNAP 475
            IT  N QL TV SISC IC+PCWNSTSD QY DGFLN N+ I+G                C+  TC+NKEAGEECCTEE CN+     A N ITAK NAP
Sbjct:  110 ITAKNTQLGTVHSISCHICNPCWNSTSDYQYTDGFLNQNLLISG----------------CNNRTCENKEAGEECCTEEQCNSAMKSNAPNGITAKGNAP 193          

HSP 2 Score: 49.2914 bits (116), Expect = 6.432e-31
Identity = 25/31 (80.65%), Postives = 27/31 (87.10%), Query Frame = 3
Query:  480 NIKERNVISILPEFNRIICSAVWLINSNILF 572
            N  ERN+ISIL EFNRIICS VWLI+SNILF
Sbjct:  224 NKYERNIISILLEFNRIICSVVWLIHSNILF 254          

HSP 3 Score: 108.612 bits (270), Expect = 2.531e-28
Identity = 60/93 (64.52%), Postives = 63/93 (67.74%), Query Frame = 2
Query:  161 MLLKAFLFIAITVVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNMRITGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNA 439
            M LKAFLFIAI V NIQL TV SISC  C  CWNS  DD      ++   R   CKSCR  IKNNI+ KSCSE TCDNK A EECCTEE CNA
Sbjct:    1 MRLKAFLFIAIAVFNIQLGTVHSISCIKCGLCWNSDRDD------MDQTSRQHNCKSCRKIIKNNILSKSCSENTCDNKGADEECCTEEFCNA 87          
The following BLAST results are available for this feature:
BLAST of SMED30012398 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 SMED30012398 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 SMED30012398 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 SMED30012398 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 SMED30012398 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 SMED30012398 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 SMED30012398 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 SMED30012398 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 SMED30012398 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 SMED30012398 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 SMED30012398 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 SMED30012398 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 SMED30012398 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 SMED30012398 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000042071.19.156e-8199.15SMESG000042071.1[more]
SMESG000042755.14.006e-7895.76SMESG000042755.1[more]
SMESG000042052.12.498e-7689.09SMESG000042052.1[more]
SMESG000042059.11.607e-7388.18SMESG000042059.1[more]
SMESG000057926.16.432e-3157.00SMESG000057926.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012398 ID=SMED30012398|Name=SMED30012398|organism=Schmidtea mediterranea sexual|type=transcript|length=748bp
CAGATCAAATTTTCATGAAATGCAAGTCAAAAGAAAATTAATGTAAAATA
TTCAGCTTATGATATTCACATTGACAATAAAATGGAGATAAAATAAAATC
GGCCATTAATATTGGACATATTTCAGGTATAAATGTTCTAATGATGAATG
GAATCCAAAAATGCTACTGAAAGCGTTTCTCTTCATTGCTATCACGGTAG
TTAATATTCAACTACGCACCGTTGAATCGATTAGCTGCAAAATTTGCAGC
CCATGCTGGAACTCTACCTCAGACGACCAGTATGATGATGGATTCCTAAA
CGGGAATATGCGAATAACTGGTTGCAAGTCTTGTCGAACAAATATTAAAA
ACAATATTATAATGAAGTCCTGTAGCGAAGAAACCTGTGATAATAAGGAG
GCAGGGGAAGAATGTTGCACTGAAGAACTATGTAATGCTGCGAAGAACAG
CATAACTGCTAAAAGTAATGCACCAAGAAAATATAAAAGAAAGAAATGTT
ATTTCAATTTTGCCTGAATTTAATAGAATCATCTGTTCAGCAGTCTGGTT
GATCAATTCGAATATTTTGTTTGAATTATTTATATATTACTAGTGCAAAT
CCTTTCATATTTGAACAATTTATTTCCAGCTTTGACACTATTCAGCAACA
TCGAGTCGTTTTATTTAATGAAATTATTCATTATAGCTTGTTTATCTATT
TATATCAAGAAATGAAATTTTTTACTAATAAATAAAAATTATGTCTAA
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protein sequence of SMED30012398-orf-1

>SMED30012398-orf-1 ID=SMED30012398-orf-1|Name=SMED30012398-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=119bp
MLLKAFLFIAITVVNIQLRTVESISCKICSPCWNSTSDDQYDDGFLNGNM
RITGCKSCRTNIKNNIIMKSCSEETCDNKEAGEECCTEELCNAAKNSITA
KSNAPRKYKRKKCYFNFA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..23
score: 0.655