SMED30004019

Overview
NameSMED30004019
Smed IDSMED30004019
Length (bp)586
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 SMED30004019 (SMED30004019) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004019 (SMED30004019) 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 SMED30004019 (SMED30004019) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004019 (SMED30004019) 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




SMED30004019

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30004019h1SMcG0014742 SmedASXL_070222SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30004019h1SMcG0014742 SmedASXL_011354SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30004019h1SMcG0014742 dd_Smed_v4_8346_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30004019h1SMcG0014742 dd_Smed_v4_8346_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30004019h1SMcG0014742 dd_Smed_v4_8346_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30004019h1SMcG0014742 dd_Smed_v4_8346_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
SMED30004019 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001463:4328..4913 +2894
v31.010305:2902..3476 -2725
Homology
BLAST of SMED30004019 vs. TrEMBL
Match: A0A2P8ZGF9 (Uncharacterized protein OS=Blattella germanica OX=6973 GN=C0J52_04068 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 6.252e-11
Identity = 35/98 (35.71%), Postives = 59/98 (60.20%), Query Frame = 3
Query:   81 VFDQVVHKILDSWTALNMAIEY--GGHSRPEVLTHFKNHIYENLPR-IAAVDDLEIILDDYMDSKFDMLCEDNSPREISILIFKYQNQSDEKLLEILN 365
            +F  VV ++ ++WTAL +A+E+  GG    EV     N I E   +   +V+D+   L DYMDS+F  +CEDNSP E++ +++++  +  E  +E +N
Sbjct:    7 LFTTVVERVFNNWTALRLAVEHNMGGFQSKEVALQLVNIITEMFKKHNVSVEDIADFLIDYMDSEFQTICEDNSPDEVAAVLWQFHQKYLEGNVEFIN 104          
BLAST of SMED30004019 vs. TrEMBL
Match: A0A1B0DBK6 (Uncharacterized protein OS=Phlebotomus papatasi OX=29031 PE=4 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 1.309e-10
Identity = 38/101 (37.62%), Postives = 56/101 (55.45%), Query Frame = 3
Query:   84 FDQVVHKILDSWTALNMAIEYG--GHSRPEVLTHFKNHIYENL--PRIAAVDDLEIILDDYMDSKFDMLCEDNSPREISILIFKYQNQ-SDEKLLEILNSL 371
            F ++V  I + WTAL +A+E+G  G +  +      NH ++    P   A +DL+  LDDY+D +F  +C+DNS +EIS  + KY N      L EI N L
Sbjct:    8 FREIVENIFNRWTALKLAVEHGMGGRTGHQKAIELMNHTFDYCIQPNTPAPEDLQDALDDYLDQEFQTICDDNSSQEISFCLIKYLNMFRAGHLAEISNEL 108          
BLAST of SMED30004019 vs. TrEMBL
Match: A0A1L8DFN3 (Putative pre-rrna-processing protein tsr2 OS=Nyssomyia neivai OX=330878 PE=4 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 2.258e-9
Identity = 30/90 (33.33%), Postives = 53/90 (58.89%), Query Frame = 3
Query:   69 GMSVVFDQVVHKILDSWTALNMAIEYG--GHSRPEVLTHFKNHIYE--NLPRIAAVDDLEIILDDYMDSKFDMLCEDNSPREISILIFKY 326
            G S  F ++V  I + W+AL +A+E+G  GHS  +      NH Y+    P+    +D++  LD+Y+D +F  +C+D+S +E+S  + +Y
Sbjct:    3 GPSEQFREIVENIFNRWSALKLAVEHGMGGHSGLQKAIELMNHTYDYCTQPKTPEQEDIQDALDEYLDQEFQTICDDDSSKEVSYYLIRY 92          
BLAST of SMED30004019 vs. TrEMBL
Match: A0A448WVD5 (Uncharacterized protein OS=Protopolystoma xenopodis OX=117903 GN=PXEA_LOCUS14586 PE=4 SV=1)

HSP 1 Score: 63.1586 bits (152), Expect = 3.421e-9
Identity = 36/116 (31.03%), Postives = 68/116 (58.62%), Query Frame = 3
Query:   84 FDQVVHKILDSWTALNMAIE--YGGHSRPEVLTHFKNHIYENLPRIAAVDDLEIILDDYMDSKFDMLCEDNSPREISILIFK----YQNQSDEKLLEILNSLPDKSDARQSIVNNE 413
            + + V K+L SWT L +A E  +GG + P+ ++ F   I E L R    D++  +LD+Y++SK ++LC+D S  E+S L+F+    ++    ++L+  ++S+P   D +  + + E
Sbjct:    4 YREYVTKVLASWTTLRLAEEHMFGGPNTPQKISDFLRDIPELLIRTRCKDEVCNMLDNYLNSKLNVLCDDGSQYEVSRLLFEGKELHRRGLVDELVRKIDSIPSPCDIKSCVADEE 119          
BLAST of SMED30004019 vs. TrEMBL
Match: D6WGF1 (Uncharacterized protein OS=Tribolium castaneum OX=7070 GN=TcasGA2_TC003011 PE=4 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 7.874e-9
Identity = 33/90 (36.67%), Postives = 55/90 (61.11%), Query Frame = 3
Query:   72 MSVVFDQVVHKILDSWTALNMAIEY---GGHSRPEVLTHFKNHIYENLPRIAAVD--DLEIILDDYMDSKFDMLCEDNSPREISILIFKY 326
            M   F +VV  I  +WTAL +A+EY   GG+ + EV+  F N+  +     + VD   ++  LDD +D +FD +CED S REI+++++++
Sbjct:    1 MEEAFGRVVQHIFSNWTALKLAVEYSESGGNPK-EVVNDFINYTTQYCLYESNVDPDGIQEALDDILDQEFDTICEDGSTREIALVLYRF 89          
BLAST of SMED30004019 vs. Planmine SMEST
Match: SMESG000075505.1 (SMESG000075505.1)

HSP 1 Score: 239.195 bits (609), Expect = 1.161e-81
Identity = 115/115 (100.00%), Postives = 115/115 (100.00%), Query Frame = 3
Query:   72 MSVVFDQVVHKILDSWTALNMAIEYGGHSRPEVLTHFKNHIYENLPRIAAVDDLEIILDDYMDSKFDMLCEDNSPREISILIFKYQNQSDEKLLEILNSLPDKSDARQSIVNNET 416
            MSVVFDQVVHKILDSWTALNMAIEYGGHSRPEVLTHFKNHIYENLPRIAAVDDLEIILDDYMDSKFDMLCEDNSPREISILIFKYQNQSDEKLLEILNSLPDKSDARQSIVNNET
Sbjct:    1 MSVVFDQVVHKILDSWTALNMAIEYGGHSRPEVLTHFKNHIYENLPRIAAVDDLEIILDDYMDSKFDMLCEDNSPREISILIFKYQNQSDEKLLEILNSLPDKSDARQSIVNNET 115          
The following BLAST results are available for this feature:
BLAST of SMED30004019 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 SMED30004019 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 SMED30004019 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 SMED30004019 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 SMED30004019 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 SMED30004019 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 SMED30004019 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 SMED30004019 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2P8ZGF96.252e-1135.71Uncharacterized protein OS=Blattella germanica OX=... [more]
A0A1B0DBK61.309e-1037.62Uncharacterized protein OS=Phlebotomus papatasi OX... [more]
A0A1L8DFN32.258e-933.33Putative pre-rrna-processing protein tsr2 OS=Nysso... [more]
A0A448WVD53.421e-931.03Uncharacterized protein OS=Protopolystoma xenopodi... [more]
D6WGF17.874e-936.67Uncharacterized protein OS=Tribolium castaneum OX=... [more]
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BLAST of SMED30004019 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 SMED30004019 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 SMED30004019 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 SMED30004019 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 SMED30004019 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 SMED30004019 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000075505.11.161e-81100.00SMESG000075505.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004019 ID=SMED30004019|Name=SMED30004019|organism=Schmidtea mediterranea sexual|type=transcript|length=586bp
CAAATATCTGTATAAAAATCATTGTTTAAATAATCAATAGTATTGTTAAT
TAATCGACAAAATATTTAGGAATGAGCGTGGTTTTTGATCAAGTTGTACA
CAAGATTTTGGATTCATGGACAGCTTTGAATATGGCAATAGAATATGGTG
GACATTCAAGACCCGAAGTTTTAACACATTTCAAAAATCATATTTATGAA
AATTTACCGAGAATCGCTGCCGTTGATGATTTAGAAATAATTCTTGATGA
TTATATGGATTCAAAATTTGATATGCTTTGCGAAGATAACAGTCCACGAG
AAATATCCATTTTAATATTTAAATATCAAAATCAGTCAGATGAAAAATTA
CTAGAAATTTTAAATTCCTTACCCGATAAATCAGATGCTAGACAATCAAT
TGTAAATAACGAGACTGATGAAGAAGATGATTTGGATGATTTGTCTGAAG
AAGACAGTATGGAAGAAATTACAGATTCTAGTGATAGTAATTCTGAAATG
GACATGGAATAAATATAAAATTCGAAATAACTGATCTGTTTTTATAAAGT
TATTCTAATTTTAGTATTTGTTTCTAACATATGTTT
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protein sequence of SMED30004019-orf-1

>SMED30004019-orf-1 ID=SMED30004019-orf-1|Name=SMED30004019-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=147bp
MSVVFDQVVHKILDSWTALNMAIEYGGHSRPEVLTHFKNHIYENLPRIAA
VDDLEIILDDYMDSKFDMLCEDNSPREISILIFKYQNQSDEKLLEILNSL
PDKSDARQSIVNNETDEEDDLDDLSEEDSMEEITDSSDSNSEMDME*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0000429neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR019398Pre-rRNA_process_TSR2
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR019398Pre-rRNA-processing protein TSR2PFAMPF10273WGGcoord: 5..79
e-value: 7.8E-13
score: 48.9
IPR019398Pre-rRNA-processing protein TSR2PANTHERPTHR21250UNCHARACTERIZEDcoord: 4..140
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 105..146
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 115..146
NoneNo IPR availablePANTHERPTHR21250:SF0PRE-RRNA-PROCESSING PROTEIN TSR2 HOMOLOGcoord: 4..140