SMED30012162

Overview
NameSMED30012162
Smed IDSMED30012162
Length (bp)855
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 SMED30012162 (SMED30012162) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012162 (SMED30012162) 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 SMED30012162 (SMED30012162) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30012162 (SMED30012162) 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



SMED30012162

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
X2 cellSMED30012162 SmedASXL_007763SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Category 2 cellSMED30012162SMESG000074058.1 dd_Smed_v4_12328_1_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
SMED30012162 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.022790:1812..2692 +4161
v31.015860:2093..2969 +3870
v31.011718:13565..14580 -3838
v31.012667:590..1602 +3832
Homology
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BLAST of SMED30012162 vs. Planmine SMEST
Match: SMESG000012603.1 (SMESG000012603.1)

HSP 1 Score: 65.855 bits (159), Expect = 4.916e-24
Identity = 32/53 (60.38%), Postives = 36/53 (67.92%), Query Frame = 1 
Query:  439 E*GKNVMQFNSSAVAQCRQILWDYGYKVSKPANALWSARSGSLEDINLHSIAI 597
            E G+ +MQFNS   AQCRQILWDYGY V+        A  GS EDIN+HSIAI
Sbjct:  114 EQGRKIMQFNSYTTAQCRQILWDYGYTVTTEL-----APPGSPEDINIHSIAI 161

HSP 2 Score: 60.4622 bits (145), Expect = 4.916e-24
Identity = 36/88 (40.91%), Postives = 50/88 (56.82%), Query Frame = 2 
Query:  176 KKTQYAKRKPENRTREQQSQGTPRKIVNDSNAYPMIPELLPQISTHESKKLCLHHITFYETFYNKKQRNDCYQSERKPQGIEIKRHAS 439
            +KT+   ++P    +EQQ QG P+KIVN SN   ++PEL+PQIS HE                   Q N+ YQ  +K +GIEI++HAS
Sbjct:   44 EKTRDTNQRPAKWFKEQQRQGAPQKIVNASNTSSLMPELMPQISKHE------------------MQHNNYYQPYQKSRGIEIEQHAS 113

HSP 3 Score: 23.483 bits (49), Expect = 4.916e-24
Identity = 9/12 (75.00%), Postives = 9/12 (75.00%), Query Frame = 1 
Query:  112 PD*IRNEVVGDA 147
            PD IRNEV GD 
Sbjct:    2 PDCIRNEVAGDT 13
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BLAST of SMED30012162 vs. Planmine SMEST
Match: SMESG000004514.1 (SMESG000004514.1)

HSP 1 Score: 79.337 bits (194), Expect = 4.263e-18
Identity = 48/118 (40.68%), Postives = 68/118 (57.63%), Query Frame = 1 
Query:  448 KNVMQFNSSAVAQCRQILWDYGYKVSKPANALWSARSGSLEDINLHSIAIKREPVGIPPKNR--------I*LTPTK*RGQTITKQTMDGPKNVVPKI-LEIAAGRIPCSYSYAPEYN 774
            + ++QF+S+A AQCR ILWDY Y VS P ++   AR G +ED+++  IAIKREP   P +          + L   + R Q   +     P+  + KI  +IAAGRI C+  YAP+YN
Sbjct:   27 REIIQFSSTASAQCRHILWDYEYSVSTPGDSTLPARPGLIEDLDIPGIAIKREPGRNPARETRQKVEFYLLLLVEEERRLQHRRRM----PQVELDKINRDIAAGRILCTGVYAPDYN 140
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BLAST of SMED30012162 vs. Planmine SMEST
Match: SMESG000074058.1 (SMESG000074058.1)

HSP 1 Score: 76.2554 bits (186), Expect = 2.777e-17
Identity = 48/114 (42.11%), Postives = 65/114 (57.02%), Query Frame = 1 
Query:  457 MQFNSSAVAQCRQILWDYGYKVSKPANALWSARSGSLEDINLHSIAIKREPVGIPPKN-----RI*LTPTK*RGQTITKQTMDGPKNVVPKILEIAAGRIPCSYSYAPEYNVSY 783
            MQF+S+  AQCRQILWDY Y V+  ++ L     GSL+++N+HSI IKR+P   P +         L   +   Q   ++ M   + +     EIAAG I C  +YAPEYNVSY
Sbjct:    1 MQFDSNTAAQCRQILWDYRYMVTTRSDPL-----GSLKEMNIHSITIKRKPGRNPAREARQRVEYYLFRLEKNRQLQHRRRM-AQRELCRINFEIAAGIILCLDTYAPEYNVSY 108
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BLAST of SMED30012162 vs. Planmine SMEST
Match: SMESG000065931.1 (SMESG000065931.1)

HSP 1 Score: 62.7734 bits (151), Expect = 1.085e-11
Identity = 38/115 (33.04%), Postives = 58/115 (50.43%), Query Frame = 1 
Query:  454 VMQFNSSAVAQCRQILWDYGYKVSKPANALWSARSGSLEDINLHSIAIKREPVG-----IPPKNRI*LTPTK*RGQTITKQTMDGPKNVVPKILEIAAGRIPCSYSYAPEYNVSY 783
            + +F + A A+CRQ +WD G+ +S      +    GS ED+ L  +AIKREP G     I  +    L   +   +   +Q +   + +     +IA GRIP +  YAP YNVS+
Sbjct:   22 IARFPAHAAARCRQAMWDAGFSISTVRETRF-GNQGSSEDVELPYVAIKREPGGNLAREIRGQAEFLLGRLEEHQKETERQIIKARRYLAQVNKDIAEGRIPSTDGYAPSYNVSF 135
[Close]
BLAST of SMED30012162 vs. Planmine SMEST
Match: SMESG000013157.1 (SMESG000013157.1)

HSP 1 Score: 61.6178 bits (148), Expect = 6.349e-11
Identity = 39/122 (31.97%), Postives = 64/122 (52.46%), Query Frame = 1 
Query:  436 IE*GKNVMQFNSSAVAQCRQILWDYGYKVSKPANALWSARSGSLEDINLHSIAIKREPVGIPPKNRI*-----LTPTK*RGQTITKQTMDGPKNVVPKILE-IAAGRIPCSYSYAPEYNVSY 783
            I+  + + +F + + A+CRQ +WD G+ +  P         G   +++L  +AIKREP G  P   +      L     R Q  T + ++  +  + ++ E IAAGRIP +  YAP+YNVS+
Sbjct:   93 IDASRVIARFPAHSAARCRQAMWDAGFSIF-PVRETRGGTQGDSNEVDLSYVAIKREP-GRSPAREMRGQAEYLLARLERHQAETNRQVEQARQYLRRVNEDIAAGRIPSTDGYAPQYNVSF 212
The following BLAST results are available for this feature:
BLAST of SMED30012162 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 SMED30012162 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 SMED30012162 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 SMED30012162 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 SMED30012162 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 SMED30012162 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 SMED30012162 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 SMED30012162 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 SMED30012162 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 SMED30012162 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 SMED30012162 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 SMED30012162 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 SMED30012162 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 SMED30012162 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000012603.14.916e-2460.38SMESG000012603.1[more]
SMESG000004514.14.263e-1840.68SMESG000004514.1[more]
SMESG000074058.12.777e-1742.11SMESG000074058.1[more]
SMESG000065931.11.085e-1133.04SMESG000065931.1[more]
SMESG000013157.16.349e-1131.97SMESG000013157.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012162 ID=SMED30012162|Name=SMED30012162|organism=Schmidtea mediterranea sexual|type=transcript|length=855bp
CAATGATGCTCATTTCATAACGTAGTAATATACGTAATAATCATACTAGA
TAATACGCACACCCAAGTAATATCAATGACAAGCAGATAAAAATTTAACA
ATGAAAATACGCCTGACTGAATTAGAAATGAGGTGGTCGGTGATGCAGGA
GAGAAGAGATATTAGCATGGATAACAAAAAAACCCAATACGCGAAACGAA
AACCAGAGAACAGGACCAGAGAGCAACAGAGCCAAGGAACCCCCCGGAAA
ATCGTCAATGACTCAAATGCGTATCCAATGATTCCAGAATTACTGCCACA
AATTTCAACACACGAAAGTAAGAAATTGTGTTTACATCATATCACCTTTT
ACGAGACATTTTATAATAAAAAGCAACGTAATGATTGTTACCAATCCGAA
CGAAAACCACAAGGAATCGAGATCAAACGGCATGCATCGAATAAGGAAAA
AATGTCATGCAATTTAATTCAAGTGCGGTAGCCCAATGCCGTCAAATCCT
ATGGGACTATGGGTACAAGGTCTCTAAACCAGCAAATGCTTTGTGGTCAG
CCCGATCAGGATCGCTGGAAGATATCAACCTCCACAGCATTGCAATCAAA
AGGGAGCCTGTTGGAATACCGCCAAAGAATAGAATTTAACTTACACCGAC
TAAATGAAGAGGACAAACAATTACAAAACAAACGATGGATGGCCCAAAGA
ATGTTGTGCCAAAAATCCTTGAAATAGCCGCAGGCAGAATTCCCTGTTCA
TATTCATATGCTCCGGAATATAATGTTTCGTATATATAATGAAACCCCGA
TTCAAGAGACTGTGATTCAACAAATGGATTTAGCCGTTCCGTGAGATCGG
AAGAG
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protein sequence of SMED30012162-orf-1

>SMED30012162-orf-1 ID=SMED30012162-orf-1|Name=SMED30012162-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=127bp
MKIRLTELEMRWSVMQERRDISMDNKKTQYAKRKPENRTREQQSQGTPRK
IVNDSNAYPMIPELLPQISTHESKKLCLHHITFYETFYNKKQRNDCYQSE
RKPQGIEIKRHASNKEKMSCNLIQVR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0002111X2 cell