SMED30016631

Overview
NameSMED30016631
Smed IDSMED30016631
Length (bp)1882
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 SMED30016631 (SMED30016631) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016631 (SMED30016631) 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 SMED30016631 (SMED30016631) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016631 (SMED30016631) 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



SMED30016631

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30016631SMESG000016293.1 SmedASXL_060826SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30016631SMESG000016293.1 SmedASXL_060826SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30016631 SmedASXL_077648SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30016631 SmedASXL_077648SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
gutSMED30016631SMESG000016297.1 SMESG000016293.1 dd_Smed_v4_2084_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30016631SMESG000016297.1 SMESG000016293.1 dd_Smed_v4_2084_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30016631SMESG000016297.1 SMESG000016293.1 dd_Smed_v4_2084_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
SMED30016631 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000144:131113..132992 -9308
Homology
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BLAST of SMED30016631 vs. Planmine SMEST
Match: SMESG000016293.1 (SMESG000016293.1)

HSP 1 Score: 154.451 bits (389), Expect = 5.885e-45
Identity = 74/75 (98.67%), Postives = 75/75 (100.00%), Query Frame = -3 
Query:  774 MRKELSKHSSRNCGAKHPDIADRSRDSEGKVYPDRAISGQECIPTIDSMPERLLVTYPLVFAKSQVAYREAIKPS 998
            MRKELSKHSSRNCGAKHPDIADRSRDSEGKVYPDRAISGQ+CIPTIDSMPERLLVTYPLVFAKSQVAYREAIKPS
Sbjct:    1 MRKELSKHSSRNCGAKHPDIADRSRDSEGKVYPDRAISGQKCIPTIDSMPERLLVTYPLVFAKSQVAYREAIKPS 75
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BLAST of SMED30016631 vs. Planmine SMEST
Match: SMESG000013207.1 (SMESG000013207.1)

HSP 1 Score: 48.9062 bits (115), Expect = 1.408e-11
Identity = 20/44 (45.45%), Postives = 32/44 (72.73%), Query Frame = -1 
Query:  839 RETVELNTRILQIGREIQKVKSTRIEPSRAKNAYLQLIACQKGY 970
            +E  EL++++ Q+ REIQK++ST  EP+R K  Y +L A Q+G+
Sbjct:   16 KENTELHSQLFQMSREIQKIRSTSGEPTRMKTTYQRLTAAQRGW 59

HSP 2 Score: 40.0466 bits (92), Expect = 1.408e-11
Identity = 23/47 (48.94%), Postives = 31/47 (65.96%), Query Frame = -3 
Query:  693 TYPLVFAKSQVAYREAIKPS*SVATKIS*PGPEKSERAKQRIRLTTD 833
            TYPLVFA  Q+AYR+AI  +  VA+  S   P K+ER K+R +  T+
Sbjct:   90 TYPLVFAPVQIAYRDAISTTKLVASLRSQRRPGKAERVKRRAQQATE 136
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BLAST of SMED30016631 vs. Planmine SMEST
Match: SMESG000031362.1 (SMESG000031362.1)

HSP 1 Score: 47.3654 bits (111), Expect = 2.191e-10
Identity = 20/44 (45.45%), Postives = 35/44 (79.55%), Query Frame = -1 
Query:  839 RETVELNTRILQIGREIQKVKSTRIEPSRAKNAYLQLIACQKGY 970
            +E VEL++++LQ+ REIQ++++  IEP++AK  Y +L A Q+G+
Sbjct:   16 QENVELHSQMLQLNREIQQIRAFLIEPAKAKRIYQRLTAAQRGW 59

HSP 2 Score: 37.3502 bits (85), Expect = 2.191e-10
Identity = 22/41 (53.66%), Postives = 28/41 (68.29%), Query Frame = -3 
Query:  714 VTYPLVFAKSQVAYREAIKPS*SVATKIS*PGPEKSERAKQ 836
            VTYPLVF+ +Q+AYREA   +   A K +   P K+ERAKQ
Sbjct:   89 VTYPLVFSPAQLAYREATNAT-KQAMKPAQRRPGKAERAKQ 128
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BLAST of SMED30016631 vs. Planmine SMEST
Match: SMESG000036641.1 (SMESG000036641.1)

HSP 1 Score: 47.3654 bits (111), Expect = 2.916e-10
Identity = 21/47 (44.68%), Postives = 34/47 (72.34%), Query Frame = -1 
Query:  839 NILRETVELNTRILQIGREIQKVKSTRIEPSRAKNAYLQLIACQKGY 979
            N  +E  EL+ +++Q+ REIQK+++T IEP+RAK    +L A Q+G+
Sbjct:  169 NSRKENTELHNQLIQMSREIQKIRATWIEPARAKAINQRLTAAQRGW 215

HSP 2 Score: 36.965 bits (84), Expect = 2.916e-10
Identity = 22/48 (45.83%), Postives = 28/48 (58.33%), Query Frame = -3 
Query:  693 VTYPLVFAKSQVAYREAIKPS*SVATKIS*PGPEKSERAKQRIRLTTD 836
            VTY LV A +Q+AYR+A   +  V  K     P K+ERAK R +  TD
Sbjct:  245 VTYQLVIAPAQIAYRDASSTTKPVTAKRPQQRPGKTERAKHRAQQATD 292
[Close]
BLAST of SMED30016631 vs. Planmine SMEST
Match: SMESG000031748.1 (SMESG000031748.1)

HSP 1 Score: 42.3578 bits (98), Expect = 1.219e-9
Identity = 23/42 (54.76%), Postives = 30/42 (71.43%), Query Frame = -3 
Query:  711 VTYPLVFAKSQVAYREAIKPS*SVATKIS*PGPEKSERAKQR 836
            VTYPLVFA +Q+AYR+ + PS S   K +   P K+ERAK+R
Sbjct: 1345 VTYPLVFAPAQLAYRDTLDPSTS-KDKPNRHRPGKAERAKRR 1385

HSP 2 Score: 39.6614 bits (91), Expect = 1.219e-9
Identity = 18/40 (45.00%), Postives = 28/40 (70.00%), Query Frame = -1 
Query:  839 ELNTRILQIGREIQKVKSTRIEPSRAKNAYLQLIACQKGY 958
            +L+ ++LQ+ REI ++K T +EP R K  Y +L A QKG+
Sbjct: 1276 DLHHQLLQLTREIPQIKGTWMEPKRVKVVYQRLEAAQKGW 1315
The following BLAST results are available for this feature:
BLAST of SMED30016631 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 SMED30016631 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 SMED30016631 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 SMED30016631 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 SMED30016631 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 SMED30016631 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 SMED30016631 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 SMED30016631 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 SMED30016631 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 SMED30016631 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 SMED30016631 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 SMED30016631 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 SMED30016631 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 SMED30016631 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000016293.15.885e-4598.67SMESG000016293.1[more]
SMESG000013207.11.408e-1145.45SMESG000013207.1[more]
SMESG000031362.12.191e-1045.45SMESG000031362.1[more]
SMESG000036641.12.916e-1044.68SMESG000036641.1[more]
SMESG000031748.11.219e-954.76SMESG000031748.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016631 ID=SMED30016631|Name=SMED30016631|organism=Schmidtea mediterranea sexual|type=transcript|length=1882bp
CTCTTCCGATCTCACGGTTGTTTAGAATGGAGAAATACGACAGAGCCACG
GATTATTGGGACAAGACTAACAAATTTTTACCTTAGAAACTCATGCAGTA
AAGCACAATGGAGCTAGAGCAATCAAACCCAGAATGTCAAGGGAGCATTA
CCGAGCCAAATCGACATAATAATACAATGGGGCGTCTGGCGAAAATACCC
CAGACGCTCCGTGATATCAACTACTCATAGGCCTATAAGCACCCGATAGC
ACATTCATCCCCAATAATAAACACGAAAATCAAAACTTAAAATCAATTCG
TGTAATTTCTTAAACCGGAATTTATTCGCAGTAAAGATTTCATTTCAGTA
AAGTGGAGGGTTAGTGGTTTATGACTTTGTTACCAAAAAATACAAAGATC
AAACCATTCATTGGTTACTCGTTGCTAGGCAAAGACTACTAAGGCCCGGC
CTCATAATGGGTTCATCAACGCCACTAGAAAGCCTGTGCTCGATTTTCTC
TATTCGGTCCTTTCTTCACATACTTAGACTCTGTACCTCCATTATCTACT
AGGTTAAAACTTCATGTGTTTTTAGGGGTCATCGTAATTCGACAAGAAAA
TCGACTAAATTAAAAGGTCCTGAACATTTATTTTAATTAAAACAACATTC
TTCAGGTATTTTAGTCCAACGATTCTGTTGGTCAGAATTTCAATCGGTTG
TCAGCCGAATCCGTTGTTTAGCACGCTCAGATTTTTCCGGTCCTGGCTAT
GATATTTTTGTTGCCACTGATCAGCTTGGTTTAATTGCTTCCCGGTATGC
TACCTGAGATTTGGCGAAGACTAGTGGATACGTTACTAGTAGCCTTTCTG
GCATGCTATCAATTGTAGGTATGCATTCTTGGCCCGAGATGGCTCGATCC
GGGTAGACTTTACCTTCTGAATCTCTCGACCTATCTGCAATATCCGGGTG
TTTAGCTCCACAGTTTCGCGAAGAATGTTTGGATAGTTCCTTTCTCATTG
AGCGTATGATGTCCCTCAACCCTCGTCTATCGTCGCATCTGTTATGGGTG
CATTTAATGGCTCCACATTGTACTCATTACCTCATTTCGTGGTTATCATT
CACTTATTTTCCAGAGTTTATTTAAATTACTTACCCAAGGTAGATCTTAA
CTTTTGTATCAAAACCTTCGTGAGCACTACAATTTGTACAGGGTAGCCAC
TTGTTTCTCGCTGGCTGATTCCATTATGCTTTTTTGTATGGTGGAAAAAG
AAAGAAAATTAAAATAAACAGGTTAAATTTAATGCACCAATAAAGTATGA
ATTTGCAGGCCATTAATTCATTTTTTCAGACACAAATATTTTATTTATAA
TACAAAGTAATTTTTCAATTATATTCAATTACTAGCATCGGAGTTTTTAT
ACTCATCATATTAAACTATATCCATTCTTTAGCTTTCCAAATTTTTTGTT
TAAATTAGCAATTTTGATATTAGTTTTTAACCGTGACCGTACAAAGCCGT
GCAAGCGATGCCGCAAAATTGATTTAGCGCGAGTGACACCGCGTAGCCGC
TCTATGGAAAAATAATTTCTAAAATGTTTAAAAATATACTAAAACGAAAT
AAAAAATGGATATGTTAAAAATAAATAGTAATTTATTCATAATAAAAGCA
TTTCATTCCGTTAACTTTAATAATAAAAGGTTTAAAAAAACACATTTTTT
TATAAACAAGACATGAAAAATTTAATAAAAAACTTACATTTTCGTACAAT
AAATTTTATTTTTACCTGCTGTTGAAAATATATAATAAAAACCAAAAAAA
TCTGAATCCGCAATAAATAATTGAAACTTCTCCAATGACCTTCGATAAGG
AACTAATCATTTATGAAAATCTATTCCAGTTT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0002109X1 cell
PLANA:0002111X2 cell
PLANA:0003116parenchymal cell