SMED30014983

Overview
NameSMED30014983
Smed IDSMED30014983
Length (bp)1460
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 SMED30014983 (SMED30014983) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014983 (SMED30014983) 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 SMED30014983 (SMED30014983) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014983 (SMED30014983) 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



SMED30014983

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30014983h1SMcG0000472 SmedASXL_054446SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30014983h1SMcG0000472 SmedASXL_062448SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30014983h1SMcG0000471 dd_Smed_v4_12219_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30014983h1SMcG0000471 dd_Smed_v4_12219_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30014983h1SMcG0000471 dd_Smed_v4_12219_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014983h1SMcG0000472 Contig54641uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014983h1SMcG0000472 Contig54641newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014983h1SMcG0000471 Contig54641uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014983h1SMcG0000471 Contig54641newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30014983h1SMcG0000472 dd_Smed_v4_12219_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30014983h1SMcG0000472 dd_Smed_v4_12219_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30014983h1SMcG0000472 dd_Smed_v4_12219_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
SMED30014983 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009492:13944..15637 -6944
v31.007262:18747..20420 +6902
v31.000675:39128..40569 +4921
Homology
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BLAST of SMED30014983 vs. Planmine SMEST
Match: SMESG000026733.1 (SMESG000026733.1)

HSP 1 Score: 130.568 bits (327), Expect = 1.030e-35
Identity = 65/126 (51.59%), Postives = 88/126 (69.84%), Query Frame = 2 
Query:  161 SPELGTTLQTVIMGPGYTLSTLGDSSCPVRTGS*QDEIEVPRIAIKREPGRNPAREARQ*AEFSLYRLETSVRKFQWKVKMARRRIEKINATIASGEIPSTDGYVPDEGAHAHRSPDPLIQQSNST 538
            +P++    +  +    Y+L+TLGD+S P+R  S  +EIE+  +AIKREP RN ARE  Q AEFSLYRLE  VRKFQWKV+M +R +++INATIA+GEIPSTDGY  D G     + DP++ Q ++ 
Sbjct:   16 TPDMAAQYRQSLWDVSYSLATLGDNSWPIRDKSRDNEIELLSLAIKREPDRNLAREPCQRAEFSLYRLEELVRKFQWKVRMTQRHLKQINATIATGEIPSTDGYAQDYGLLFELN-DPVLTQMHTN 140
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BLAST of SMED30014983 vs. Planmine SMEST
Match: SMESG000058576.1 (SMESG000058576.1)

HSP 1 Score: 117.857 bits (294), Expect = 3.446e-32
Identity = 57/75 (76.00%), Postives = 62/75 (82.67%), Query Frame = 2 
Query:  263 QDEIEVPRIAIKREPGRNPAREARQ*AEFSLYRLETSVRKFQWKVKMARRRIEKINATIASGEIPSTDGYVPDEG 487
            QDEIE+P IAI  + GRNPA EARQ AEFSLYRLE  V KFQWKV+MARRR+E+INA IASGEI STDGY PD G
Sbjct:  156 QDEIEIPSIAINHKLGRNPAEEARQHAEFSLYRLEELVLKFQWKVRMARRRLEQINAAIASGEILSTDGYAPDYG 230

HSP 2 Score: 40.0466 bits (92), Expect = 3.446e-32
Identity = 17/31 (54.84%), Postives = 23/31 (74.19%), Query Frame = 3 
Query:  471 MCRMRAPTHIVLPTHLFNSPIRQQGRRDEHS 563
            + RM+A T+I+LP  LFN  +R + RRDEHS
Sbjct:  240 LTRMQALTNIILPAKLFNGSMRHRNRRDEHS 270
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BLAST of SMED30014983 vs. Planmine SMEST
Match: SMESG000052862.1 (SMESG000052862.1)

HSP 1 Score: 114.775 bits (286), Expect = 9.723e-28
Identity = 58/113 (51.33%), Postives = 78/113 (69.03%), Query Frame = 2 
Query:  206 GYTLSTLGDSSCPVRTGS*QDEIEVPRIAIKREPGRNPAREARQ*AEFSLYRLETSVRKFQWKVKMARRRIEKINATIASGEIPSTDGYVPDEGAHAHRSPDPLIQQSNSTTR 544
            GY LST GDSS P R+ S  +EIE+P I I REPG+NPAREARQ AEF+  ++E   RK+Q K  +AR+R+ ++N  IASG IPSTDG+ P+ G  +    DP ++Q  + T+
Sbjct: 2289 GYLLSTYGDSSWPRRSESQAEEIELPSIVINREPGKNPAREARQRAEFTAMKMEELERKYQRKAVLARQRLVQVNRDIASGAIPSTDGFPPEYGV-SFELDDPRLKQMTTPTK 2400

HSP 2 Score: 28.1054 bits (61), Expect = 9.723e-28
Identity = 10/25 (40.00%), Postives = 14/25 (56.00%), Query Frame = 3 
Query:  129 WRDEDQVAIRVAPNLAPHYRQSLWD 203
            W D  +V +++    A  YRQ LWD
Sbjct: 2263 WNDNSRVTLQIPSASAARYRQMLWD 2287
[Close]
BLAST of SMED30014983 vs. Planmine SMEST
Match: SMESG000052862.1 (SMESG000052862.1)

HSP 1 Score: 114.775 bits (286), Expect = 1.215e-27
Identity = 58/113 (51.33%), Postives = 78/113 (69.03%), Query Frame = 2 
Query:  206 GYTLSTLGDSSCPVRTGS*QDEIEVPRIAIKREPGRNPAREARQ*AEFSLYRLETSVRKFQWKVKMARRRIEKINATIASGEIPSTDGYVPDEGAHAHRSPDPLIQQSNSTTR 544
            GY LST GDSS P R+ S  +EIE+P I I REPG+NPAREARQ AEF+  ++E   RK+Q K  +AR+R+ ++N  IASG IPSTDG+ P+ G  +    DP ++Q  + T+
Sbjct: 2129 GYLLSTYGDSSWPRRSESQAEEIELPSIVINREPGKNPAREARQRAEFTAMKMEELERKYQRKAVLARQRLVQVNRDIASGAIPSTDGFPPEYGV-SFELDDPRLKQMTTPTK 2240

HSP 2 Score: 28.1054 bits (61), Expect = 1.215e-27
Identity = 10/25 (40.00%), Postives = 14/25 (56.00%), Query Frame = 3 
Query:  129 WRDEDQVAIRVAPNLAPHYRQSLWD 203
            W D  +V +++    A  YRQ LWD
Sbjct: 2103 WNDNSRVTLQIPSASAARYRQMLWD 2127
[Close]
BLAST of SMED30014983 vs. Planmine SMEST
Match: SMESG000027782.1 (SMESG000027782.1)

HSP 1 Score: 109.383 bits (272), Expect = 2.415e-27
Identity = 58/118 (49.15%), Postives = 78/118 (66.10%), Query Frame = 2 
Query:  191 VIMGPGYTLSTLGDSSCPVRTGS*QDEIEVPRIAIKREPGRNPAREARQ*AEFSLYRLETSVRKFQWKVKMARRRIEKINATIASGEIPSTDGYVPDEGAHAHRSPDPLIQQSNSTTR 544
            V+   GY LST GDSS P R+    +EIE+P IAIKREPG NPAREARQ AE++  ++E   RK+  K  +AR+R+ ++N  IASG IPSTDG+ P+ G  +    DP + Q  + T+
Sbjct:   57 VLWDNGYLLSTYGDSSWPRRSKYQAEEIELPSIAIKREPGHNPAREARQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGV-SFELDDPRLMQMTAPTK 173
The following BLAST results are available for this feature:
BLAST of SMED30014983 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 SMED30014983 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 SMED30014983 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 SMED30014983 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 SMED30014983 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 SMED30014983 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 SMED30014983 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 SMED30014983 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 SMED30014983 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 SMED30014983 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 SMED30014983 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 SMED30014983 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 SMED30014983 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 SMED30014983 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000026733.11.030e-3551.59SMESG000026733.1[more]
SMESG000058576.13.446e-3276.00SMESG000058576.1[more]
SMESG000052862.19.723e-2851.33SMESG000052862.1[more]
SMESG000052862.11.215e-2751.33SMESG000052862.1[more]
SMESG000027782.12.415e-2749.15SMESG000027782.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014983 ID=SMED30014983|Name=SMED30014983|organism=Schmidtea mediterranea sexual|type=transcript|length=1460bp
ACGAGGAAAATGAAGGGTCAAGCAGCAGGAGCGAATGTAGCCATCAACTC
GGACCTTCCGACCACCAGCAGGACGACACCCCGAAATGTTACGAGGAAAC
AGGAGTACGACCAACCGAAACCGCAATATGGAGAGACGAGGACCAAGTTG
CTATTCGAGTAGCCCCGAACTTGGCACCACACTACAGACAGTCATTATGG
GACCCGGATACACCCTCTCCACCTTGGGAGATAGCAGCTGTCCCGTTAGA
ACAGGTTCTTGACAGGACGAAATCGAAGTACCAAGAATCGCAATCAAACG
GGAGCCCGGCCGGAACCCGGCTCGAGAAGCGAGACAATGAGCTGAATTTT
CACTTTACAGGTTGGAAACATCGGTCCGAAAATTCCAATGGAAGGTGAAA
ATGGCGAGGAGACGCATAGAAAAAATCAATGCTACGATAGCTTCTGGCGA
GATCCCGAGCACCGACGGATATGTGCCGGATGAGGGCGCCCACGCACATC
GTTCTCCCGACCCACTTATTCAACAGTCCAATTCGACAACAAGGTAGAAG
AGATGAACATTCCTACCAGTGCCTTTACCAAAGCCGAAGACAACGAGGTC
AAGGCATGAAGCCACTCCAAGATCGAAGAGTTGGAAGATCGTTCCGATAA
AACAATAACGAACAATTACAACTTATTATTTTGATATCAATAAAGTTTAG
TTTGATTAAAGAAATTTTTCATATATCATCGTTAAATGAAATAAAACCCT
TTGAAATAAAGTCCTTTGAACGAGTTTTAATGTAGTTACCCGTAATTCCC
ATATTTAAAATGCAAATATCGAGAGACAATTACTATAACTAAATACAATG
TGAAGCCCATTGAATTAATAAGTTAAGTTCACGTTTTACATAGAGCTCTT
AAATTATGACATTATTAATACCCACGAACTCCGATTTCTACCAACGCTCG
TCGTGTCATTTTTCTACTTCAGGTATGGAATCAATTCAGGTGATAAATCA
AGAACTGTCCTGACTACGTACAACCAACCTGGACCTTCACCAACAGTTAT
TGCAAGTAAGCAAAGAATGTCAGGAGATCAAATCTACCTGGATCAAACCG
GAGCGGCGAGAAAAATTTATCAAAAGATGGATGCAGAACAACGTGGCTGG
CAAGAGGAATAGCAATTAGTACAGGCATTGCACATCCAGAAACGTGGTCT
AGAAGTAGCATTGACTGCCAGCCAAGAGGGCAACTCAGTTACCTATCCTC
TAGTTTTCGCCCCAGCTAAATCGCCCTCACTCACGACTAGGAATATCCGA
ACGAAAACGTCGTCGCTTGGTTCTAACCAATAAACCCAATAATGACAGAG
GACAAGACTAATTGAATTCATCGAATACCAAAATTAATTGATAAACTATT
ACAATGTATAGAATGAATGTATTATCCAATAATATGATAAATATAATTTT
ATAGTTGTTT
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protein sequence of SMED30014983-orf-1

>SMED30014983-orf-1 ID=SMED30014983-orf-1|Name=SMED30014983-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=132bp
EENEGSSSRSECSHQLGPSDHQQDDTPKCYEETGVRPTETAIWRDEDQVA
IRVAPNLAPHYRQSLWDPDTPSPPWEIAAVPLEQVLDRTKSKYQESQSNG
SPAGTRLEKRDNELNFHFTGWKHRSENSNGR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell