SMED30018807

Overview
NameSMED30018807
Smed IDSMED30018807
Length (bp)671
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 SMED30018807 (SMED30018807) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018807 (SMED30018807) 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 SMED30018807 (SMED30018807) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30018807 (SMED30018807) 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



SMED30018807

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
intestinal phagocyteSMED30018807SMESG000020876.1 Contig1571newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30018807SMESG000020876.1 Contig1571uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30018807SMESG000006038.1 SMESG000005903.1 SMESG000005899.1 SMESG000005759.1 SMESG000005757.1 Contig1571newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30018807SMESG000006038.1 SMESG000005903.1 SMESG000005899.1 SMESG000005759.1 SMESG000005757.1 Contig1571uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30018807SMESG000020876.1 SmedASXL_005888SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parenchymaSMED30018807SMESG000020876.1 dd_Smed_v4_12159_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30018807SMESG000020876.1 dd_Smed_v6_12159_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30018807 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.033502:3591..4261 -3301
Homology
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BLAST of SMED30018807 vs. TrEMBL
Match: A0A183SRI2 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS6830 PE=4 SV=1)

HSP 1 Score: 93.9745 bits (232), Expect = 4.832e-20
Identity = 43/92 (46.74%), Postives = 66/92 (71.74%), Query Frame = 2 
Query:  164 KNAQNSIKQTETKSLIKTQQKRKRKFPPLKRNSKLEKLIKILEDRRITDDCELYQLEDLQMPRLRRVLNIVFVSLGMLFLFGVITVIIYTGI 439
            KN Q   +++ + +     + +KR+F   +RNSKLE+LI++LED+RI D+ + YQLED++MPRLR  LNI+F++ G+ FL  V+ VI+YT I
Sbjct:  107 KNEQE--QESTSGNTAGVTEGKKRRFHAPRRNSKLERLIRLLEDKRIIDEADAYQLEDIKMPRLRNALNIIFITFGVCFLLAVVIVILYTTI 196
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BLAST of SMED30018807 vs. TrEMBL
Match: A0A3S5AFZ6 (Uncharacterized protein OS=Protopolystoma xenopodis OX=117903 GN=PXEA_LOCUS16344 PE=4 SV=1)

HSP 1 Score: 85.8853 bits (211), Expect = 2.130e-17
Identity = 36/59 (61.02%), Postives = 51/59 (86.44%), Query Frame = 2 
Query:  257 NSKLEKLIKILEDRRITDDCELYQLEDLQMPRLRRVLNIVFVSLGMLFLFGVITVIIYT 433
            NSKL+++I  LED+R+ DD ++++L+DLQMPRLRR+LNI+FV+LG+ FL  V+ VIIYT
Sbjct:  102 NSKLDRVIAFLEDKRVKDDADIHRLDDLQMPRLRRILNIIFVTLGVCFLLAVVIVIIYT 160
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BLAST of SMED30018807 vs. TrEMBL
Match: A0A183VLS9 (Uncharacterized protein OS=Trichobilharzia regenti OX=157069 GN=TRE_LOCUS1435 PE=4 SV=1)

HSP 1 Score: 84.7297 bits (208), Expect = 2.297e-16
Identity = 39/62 (62.90%), Postives = 50/62 (80.65%), Query Frame = 2 
Query:  257 NSKLEKLIKILEDRRITDDCELYQLEDLQMPRLRRVLNIVFVSLGMLFLFGVITVIIYTGIM 442
            NSKL++LI+ LED+R+ DD    +LEDLQMPRLR+VLNI+FV+LG+ FL  VI VI+YT I 
Sbjct:  166 NSKLDRLIRFLEDKRVKDDGNGEELEDLQMPRLRKVLNIIFVTLGVSFLLAVIIVILYTTIA 227
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BLAST of SMED30018807 vs. TrEMBL
Match: A0A0R3SQZ1 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS7533 PE=4 SV=1)

HSP 1 Score: 83.1889 bits (204), Expect = 2.614e-16
Identity = 43/99 (43.43%), Postives = 68/99 (68.69%), Query Frame = 2 
Query:  164 KNAQNSIKQT-ETKSLIKTQQK-------RKRKFPPLKRNSKLEKLIKILEDRRITDDCE-LYQLEDLQMPRLRRVLNIVFVSLGMLFLFGVITVIIYT 433
             + +NS+  + E  S+I  Q++       +K++F   +RNS LE+ I +LED+RI +D E  +QLED++MPRLR+VLNI+F++ G+ FL  V+ VI+YT
Sbjct:   57 NSTRNSVSDSAEDDSIIPNQRQNPSNSSTKKKRFKGPRRNSLLERFIAVLEDKRIMEDSEDAHQLEDIKMPRLRKVLNIIFITAGVCFLLAVVIVILYT 155
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BLAST of SMED30018807 vs. TrEMBL
Match: A0A4E0RZB3 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_004731 PE=4 SV=1)

HSP 1 Score: 85.1149 bits (209), Expect = 2.762e-16
Identity = 49/90 (54.44%), Postives = 69/90 (76.67%), Query Frame = 2 
Query:  191 TETKSLIKTQ------QKRKRKFPPLKRNSKLEKLIKILEDRRITDDCE-LYQLEDLQMPRLRRVLNIVFVSLGMLFLFGVITVIIYTGI 439
            TET +L+ ++      +K++R+F   +RNSKL+KLI++LED+R+ DD E   +LEDLQMPRLR+VLNI+FV+LG+ FL  VI VI+YT I
Sbjct:  164 TETMNLVDSEVATVQKEKKRRRFRRPRRNSKLDKLIRLLEDKRVGDDDENAEELEDLQMPRLRKVLNIIFVTLGVCFLLAVIIVIMYTTI 253
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BLAST of SMED30018807 vs. Planmine SMEST
Match: SMESG000020876.1 (SMESG000020876.1)

HSP 1 Score: 226.098 bits (575), Expect = 1.853e-76
Identity = 113/113 (100.00%), Postives = 113/113 (100.00%), Query Frame = 2 
Query:  113 MQSLIQNNPSIIESKPYKNAQNSIKQTETKSLIKTQQKRKRKFPPLKRNSKLEKLIKILEDRRITDDCELYQLEDLQMPRLRRVLNIVFVSLGMLFLFGVITVIIYTGIMPVS 451
            MQSLIQNNPSIIESKPYKNAQNSIKQTETKSLIKTQQKRKRKFPPLKRNSKLEKLIKILEDRRITDDCELYQLEDLQMPRLRRVLNIVFVSLGMLFLFGVITVIIYTGIMPVS
Sbjct:    1 MQSLIQNNPSIIESKPYKNAQNSIKQTETKSLIKTQQKRKRKFPPLKRNSKLEKLIKILEDRRITDDCELYQLEDLQMPRLRRVLNIVFVSLGMLFLFGVITVIIYTGIMPVS 113
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BLAST of SMED30018807 vs. Planmine SMEST
Match: SMESG000016739.1 (SMESG000016739.1)

HSP 1 Score: 107.071 bits (266), Expect = 1.384e-29
Identity = 52/86 (60.47%), Postives = 67/86 (77.91%), Query Frame = 2 
Query:  188 QTETKSLIKTQQKRKRKFPPLKRNSKLEKLIKILEDRRITDDCELYQLEDLQMPRLRRVLNIVFVSLGMLFLFGVITVIIYTGIMP 445
            Q+ ++      +K+KR+F PL  +SKL KLI  L+D+RI ++ +LYQLEDLQMPRLR+VLNIVFV LG+LFL GVI VIIYT I+P
Sbjct:   29 QSNSRKFSANNEKKKRRFQPLHPDSKLTKLITFLQDKRIKEEKDLYQLEDLQMPRLRKVLNIVFVVLGILFLLGVIIVIIYTSIVP 114
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BLAST of SMED30018807 vs. Planmine SMEST
Match: SMESG000021722.1 (SMESG000021722.1)

HSP 1 Score: 92.0485 bits (227), Expect = 7.481e-23
Identity = 46/81 (56.79%), Postives = 63/81 (77.78%), Query Frame = 2 
Query:  200 KSLIKTQQKRKRK---FPPLKRNSKLEKLIKILEDRRITDDCELYQLEDLQMPRLRRVLNIVFVSLGMLFLFGVITVIIYT 433
            ++LI+ ++K  RK   F   ++NS+LEK+I  LEDRRI +  ELYQLEDL+MP+LR+ LNI+FV+ G+LFL GVI VIIY+
Sbjct:  118 EALIEEKEKISRKKKIFSRPRKNSRLEKVINFLEDRRIKEGSELYQLEDLKMPKLRKFLNIIFVAFGILFLLGVIIVIIYS 198
The following BLAST results are available for this feature:
BLAST of SMED30018807 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 SMED30018807 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 SMED30018807 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 SMED30018807 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 SMED30018807 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 SMED30018807 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 SMED30018807 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 SMED30018807 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183SRI24.832e-2046.74Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A3S5AFZ62.130e-1761.02Uncharacterized protein OS=Protopolystoma xenopodi... [more]
A0A183VLS92.297e-1662.90Uncharacterized protein OS=Trichobilharzia regenti... [more]
A0A0R3SQZ12.614e-1643.43Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
A0A4E0RZB32.762e-1654.44Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
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BLAST of SMED30018807 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 SMED30018807 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 SMED30018807 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 SMED30018807 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 SMED30018807 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 SMED30018807 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000020876.11.853e-76100.00SMESG000020876.1[more]
SMESG000016739.11.384e-2960.47SMESG000016739.1[more]
SMESG000021722.17.481e-2356.79SMESG000021722.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018807 ID=SMED30018807|Name=SMED30018807|organism=Schmidtea mediterranea sexual|type=transcript|length=671bp
CGTTGACATAATGCTTGAATAATCTGGCTTAGCCTTTCATAATTCTTACT
TTTTTATTAAAATTTTTTTTTTATCTCAATATGCTTCTGTTTGGATGAGA
CAAAACATTTGAATGCAAAGTTTAATTCAAAACAATCCATCAATTATCGA
ATCGAAACCCTATAAAAATGCTCAGAATTCTATCAAACAAACGGAAACAA
AATCGTTAATAAAGACCCAACAAAAACGAAAGAGAAAATTTCCACCGTTG
AAACGAAACAGCAAACTCGAAAAACTTATCAAAATACTCGAAGACCGAAG
AATCACAGACGATTGTGAATTATATCAGTTGGAAGACTTACAAATGCCGA
GATTGCGACGAGTTCTTAACATTGTTTTTGTTTCGTTGGGTATGCTGTTT
CTATTTGGAGTAATAACGGTAATTATTTATACTGGAATTATGCCAGTCAG
TTAGTATATAACTTTATATATTTATATATAATAGAATTTTCCAAAATGAT
AAAGTATTGCTTGCTGTTTGTTGTTGTGTTTGCGTATTTGTTTAATATCA
CCCATGGAATCAAAATCAATGTGGCTATTATTTTTATTGTAGACATTATT
TTCATAGAGATTTTAAAAATATTCAGATCCGAATTGTTGAAATTTTTAGA
CAACCTTGTGATGACTGCATC
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protein sequence of SMED30018807-orf-1

>SMED30018807-orf-1 ID=SMED30018807-orf-1|Name=SMED30018807-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp
MQSLIQNNPSIIESKPYKNAQNSIKQTETKSLIKTQQKRKRKFPPLKRNS
KLEKLIKILEDRRITDDCELYQLEDLQMPRLRRVLNIVFVSLGMLFLFGV
ITVIIYTGIMPVS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 16..44
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 16..31
NoneNo IPR availableTMHMMTMhelixcoord: 87..109