SMED30025964

Overview
NameSMED30025964
Smed IDSMED30025964
Length (bp)2281
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 SMED30025964 (SMED30025964) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30025964 (SMED30025964) 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 SMED30025964 (SMED30025964) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30025964 (SMED30025964) 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



SMED30025964

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
nervous systemSMED30025964 dd_Smed_v4_16659_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
anterior sideSMED30025964 dd_Smed_v4_16659_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30025964 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007202:24577..26912 +10027
Homology
[Close]
BLAST of SMED30025964 vs. Planmine SMEST
Match: SMESG000042125.1 (SMESG000042125.1)

HSP 1 Score: 149.443 bits (376), Expect = 5.745e-41
Identity = 91/175 (52.00%), Postives = 117/175 (66.86%), Query Frame = -2 
Query:  238 MSNNSDLTIEHAESINIVMRNQTR*GLLELLRKNMIFMLLEFRRK*FDCENHSEAEK*LNDMEKWKKPEDQQLTTVFN*HVGDETEIVWKETKFKQKK*IFDRRSKDVVLRNIPDEK--IDSEQDPRTKLKNVKLKFARFKKRVRKLIFEV*DMSMSKEEIMQDVISKRI*NDRI 756
            MSNNSDLT +HAESIN++ R+QTR GLLE L K  IF LL+F  + FD + H EAEK L DMEKW + EDQ LTTVF+  + DE E++WKETK  Q+K + D  ++   L     ++  +   Q+  +  + +  +FA F+  VRKLI EV D  MSKEEI+QDVI KRI NDRI
Sbjct:    1 MSNNSDLTGDHAESINMITRSQTRKGLLESLPKKTIFELLDFNIRRFDGKIHLEAEKRLTDMEKWIQIEDQPLTTVFDLLLVDEAEMLWKETKSTQRKEMSDSEARMWFLETFTVKRSILSKIQELSSIKQGINERFATFEITVRKLITEVYDSGMSKEEIVQDVICKRIQNDRI 175
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BLAST of SMED30025964 vs. Planmine SMEST
Match: SMESG000016508.1 (SMESG000016508.1)

HSP 1 Score: 133.265 bits (334), Expect = 1.017e-35
Identity = 83/170 (48.82%), Postives = 107/170 (62.94%), Query Frame = -2 
Query:  253 MSNNSDLTIEHAESINIVMRNQTR*GLLELLRKNMIFMLLEFRRK*FDCENHSEAEK*LNDMEKWKKPEDQQLTTVFN*HVGDETEIVWKETKFKQKK*IFDRRSKDVVLRNIPDEK--IDSEQDPRTKLKNVKLKFARFKKRVRKLIFEV*DMSMSKEEIMQDVISKRI 756
            MSNNSDLT +H ESIN+V RNQTR GLLE L K  I  LL+   +  D + H E EK L DMEKW + EDQQLT VF+  + DE EI  KETK  Q+K + D  +K   L     ++  +   Q+  +  + +  +FA F+ RVRKLI E+ +  +SKEEI+QDVI KRI
Sbjct:    1 MSNNSDLTGDHTESINMVTRNQTRIGLLESLYKTTILELLDLNIRRLDGKRHLETEKWLTDMEKWMQTEDQQLTIVFDLLLVDEAEITLKETKSTQRKEMSDSETKMRFLETFTVKRSILSKFQELNSIKQGINERFATFEIRVRKLITELYNSGLSKEEIVQDVICKRI 170
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BLAST of SMED30025964 vs. Planmine SMEST
Match: SMESG000029259.1 (SMESG000029259.1)

HSP 1 Score: 82.8037 bits (203), Expect = 4.278e-18
Identity = 43/91 (47.25%), Postives = 59/91 (64.84%), Query Frame = -2 
Query:  967 EVLRNKWVLRIGSSKEIQVDCGECFE-----ELIKSEGIEIVFSS*HHHDINRFIKRKYCSIRNYINASLRVQIRKS*DITGCRIYYVLNS 1224
            E L NKW+L+ G+ KE+ VDCG+ FE     EL K+ GIE++FSS +HH+ N  I+R++ +IR YINASL    RK+       I Y LN+
Sbjct: 3340 ETLLNKWILKFGAPKELHVDCGKNFEARSIKELAKTAGIELIFSSPYHHNTNGIIERQFRTIREYINASLNEGGRKNWADIVPEIKYTLNA 3430

HSP 2 Score: 28.4906 bits (62), Expect = 4.278e-18
Identity = 12/18 (66.67%), Postives = 15/18 (83.33%), Query Frame = -3 
Query: 1317 STKPFEKIYIDIRGRKKQ 1370
            ST+PFEKIY+DI G  K+
Sbjct: 3289 STEPFEKIYMDICGPLKE 3306
[Close]
BLAST of SMED30025964 vs. Planmine SMEST
Match: SMESG000031418.1 (SMESG000031418.1)

HSP 1 Score: 53.1434 bits (126), Expect = 2.817e-11
Identity = 27/45 (60.00%), Postives = 35/45 (77.78%), Query Frame = -2 
Query:  238 KNVKLKFARFKKRVRKLIFEV*DMSMSKEEIMQDVISKRI*NDRI 372
            + +  +FA F+ RVRKLI EV D+ MSKE+I+QDVI KR+ NDRI
Sbjct:   25 QGINERFATFEIRVRKLITEVYDLGMSKEDIVQDVICKRMQNDRI 69

HSP 2 Score: 35.039 bits (79), Expect = 2.817e-11
Identity = 17/21 (80.95%), Postives = 17/21 (80.95%), Query Frame = -3 
Query:  375 MWF*ETFPMKRSILSKIQELS 437
            MWF ETF  KRSILSKIQ LS
Sbjct:    1 MWFFETFTDKRSILSKIQALS 21
[Close]
BLAST of SMED30025964 vs. Planmine SMEST
Match: SMESG000074789.1 (SMESG000074789.1)

HSP 1 Score: 54.6842 bits (130), Expect = 7.135e-9
Identity = 29/65 (44.62%), Postives = 41/65 (63.08%), Query Frame = -2 
Query: 1030 KWVLRIGSSKEIQVDCGECFEELIKSE-----GIEIVFSS*HHHDINRFIKRKYCSIRNYINASL 1209
            K +LR G  KEI+VDCG+ +E  +  E      I++ FSS +HH  N  I+RK+ +IR  INA+L
Sbjct:  694 KSILRFGCPKEIKVDCGKAYESTMMREFTEKLDIKLYFSSPYHHQTNGQIERKFRTIRELINATL 758

HSP 2 Score: 25.409 bits (54), Expect = 7.135e-9
Identity = 10/34 (29.41%), Postives = 22/34 (64.71%), Query Frame = -1 
Query: 1232 VEEKSSK*KTYVCDIINHFSRYISLLVIVNQDEK 1333
            + +++ + K Y+  +I+ +S+Y  L  I+ QDE+
Sbjct:  652 LPQETKRRKKYILGMIDQYSKYQILTTIIRQDEE 685
The following BLAST results are available for this feature:
BLAST of SMED30025964 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 SMED30025964 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 SMED30025964 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 SMED30025964 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 SMED30025964 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 SMED30025964 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 SMED30025964 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 SMED30025964 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 SMED30025964 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 SMED30025964 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 SMED30025964 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 SMED30025964 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 SMED30025964 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 SMED30025964 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000042125.15.745e-4152.00SMESG000042125.1[more]
SMESG000016508.11.017e-3548.82SMESG000016508.1[more]
SMESG000029259.14.278e-1847.25SMESG000029259.1[more]
SMESG000031418.12.817e-1160.00SMESG000031418.1[more]
SMESG000074789.17.135e-944.62SMESG000074789.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025964 ID=SMED30025964|Name=SMED30025964|organism=Schmidtea mediterranea sexual|type=transcript|length=2281bp
ATAATTACAAGGTATAAAACGTAATATTTGAAAAGCGTAATTGTGTAAAT
TTAAATTTTTATAATCTATTTTTAATATAGTGTAATATAGTTATGTTGGT
GCGTGGGATTTTTGTATTATTATCATAGTCTTCATAATCAGTTTCATCTA
TTGTTGAATCTNTTTCATGANTGGTTTCTGCTTCTCATGAACACAAGTTA
TTCTTTGAGATATTTTATAAGTTTTAAAAAATAGCAGTATACGATCATTC
TATATTCGTTTTGAAATAACATCCTGCATTATTTCTTCTTTCGACATACT
CATATCCTAAACTTCAAAAATTAATTTACGTACCCTTTTCTTAAACCTTG
CAAATTTTAATTTTACGTTTTTTAACTTAGTTCTTGGATCTTGCTCAGAA
TCGATCTTTTCATCGGGAATGTTTCTTAAAACCACATCCTTGCTTCGTCT
ATCAAATATTTATTTTTTCTGTTTGAATTTGGTTTCTTTCCACACGATCT
CTGTTTCGTCACCCACATGTCAGTTGAATACTGTGGTTAATTGTTGATCT
TCAGGTTTTTTCCATTTCTCCATATCATTTAACTATTTTTCAGCCTCTGA
ATGGTTTTCACAGTCAAATCACTTTCTTCTGAATTCTAGCAACATAAATA
TCATGTTTTTGCGAAGTAATTCTAATAGTCCTTAGCGAGTTTGGTTCCTC
ATTACTATATTGATTGATTCAGCGTGCTCGATCGTTAAATCAGAATTATT
TGACATGAATCCAAATATTTATTTAAGTTTTTTAAAAACTTCAAAACTAA
CAATTCCTTCAAATTTAAACATATTAGAATAATTGCGAATCATTTAAAAG
AACTTCTCCTTGTTAAAGGTACCTAACTGTGTGAAATAATGAATTTTAAA
AGATTTTGGTGTGGATTTCAAGTTATGTATTTTGTTGCTTTGGGAAATTG
ATTAATTAAAATTTCCAGAATTGAGCACATAGTATATTCTACATCCGGTA
ATATCCTAGCTTTTTCTGATCTGTACCCGTAATGATGCGTTAATATAATT
TCTTATTGAACAATACTTTCTTTTTATAAATCTATTGATGTCATGATGGT
GTTAGCTTGAAAACACTATCTCGATTCCTTCTGATTTTATCAGTTCTTCA
AAACATTCTCCACAGTCTACTTGTATTTCTTTCGATGATCCGATTCTCAG
AACCCACTTGTTTCGCAATACCTCAATATTGTTTTTCATCTTGGTTAACT
ATAACTAATAGAGAAATGTATCTACTGAAGTGATTGATGATGTCACATAC
ATATGTTTTTTATTTACTGCTTTTTTCTTCCACGTATATCTATATAAATT
TTCTCAAATGGTTTTGTACTGTTAGTAAAGAGGGTCAATTTTATTAATAT
TTTTCTAGGGTTTTTGTTTATTTTTTCATTGACTCTTATCTAAACGCCTT
CAAGATTATTATGCTATCCAATCTATGCACCCATGGTAGGATTTAATGAA
GTATTTGAATTATTTCACAAAATATTCACAACAATTCAACCCTTATTTTA
TGAAAAATTTCTTATTTTATTTATAAATCGCTATCACAACTACATCTGAT
ACCTTTCCAATCCTGACTACCTCTTTAAAGATTATATTCATGGTGCATCT
CAGTGTTACCTAATATATAATTCGTTTGTAATTCCAATAGAAGTGACGTT
TTCACGCACACCATTAGCTTCATATGGTCTACTGCGTTCCGTTTACTGCG
TTTTAACCAGAAAGTCTGGGATCCATCAAATTAACTGTGAATTCCTATTT
TTCACTACATTCTGACCTGTTAATTGTTGATGCGAGTTAACATTTTGGCA
CTTAGTCATGGTATATCCAATTTCAATTTGAAAGGGTGGAAGTAACAGAG
AAATTTCTAATAAGTGTAATAGCCAGACCTGTGAATGGTCTAAAATAGCA
ATTTCGACTTTATGTACCATATCATTCGATTTTAGAGAGATATAAGCATT
GAGGAAAACAAAACAAATAAAAAAATAAAAAAACAAACCAAAATTTTATT
ACATAACCATGAAAAATTACATTACAGAAAAATAAACTAAAACTACCTTA
CCACTTATATTAAATTGTCTGACAGTGATCGTGGGTCAGAGCTGGTAAAA
ACATGAAAATTTCAACTGAAAATAATAATAATTTAAGAATGAAACCTACG
TGTCTATTTATTTTTAATTTCTGTTTGTCTGTTCACTACTGTATCGAGCA
TTGCATATACATCCATGTCTTTCAATTCTTT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 7..29