SMED30000310

Overview
NameSMED30000310
Smed IDSMED30000310
Length (bp)2256
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 SMED30000310 (SMED30000310) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30000310 (SMED30000310) 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 SMED30000310 (SMED30000310) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30000310 (SMED30000310) 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



SMED30000310

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 cellSMED30000310 SmedASXL_008663SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30000310 SmedASXL_008663SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30000310 dd_Smed_v4_9639_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30000310 dd_Smed_v4_9639_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30000310 SMED_03125_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30000310 SMED_03125_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30000310 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001547:7711..9966 +11199
Homology
[Close]
BLAST of SMED30000310 vs. TrEMBL
Match: A0A267F3C9 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig030049g1 PE=4 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 1.815e-7
Identity = 32/93 (34.41%), Postives = 48/93 (51.61%), Query Frame = 1 
Query:   55 MAEFLHDLFSRITGNESF-LKCLKLCEIEDFSELIGLNESTFDQMETYIQKKCTQMPFNERSNFIGNNFAKNPDSFKFSPGIRQKILSLTKNL 330
            M +   +L  R TG  S  + CL+LC   +   L GL ++  D +E +++  C  MP  ER  ++G  FA  PD F+F  G R+ IL   + L
Sbjct:    1 MDDTCRELLGRYTGQSSAAINCLELCGYANARVLQGLTDAEIDNVERFVRDACQLMPQEERVAYVGQIFADCPDQFRFPAGTRKGILVGVQGL 93
[Close]
BLAST of SMED30000310 vs. TrEMBL
Match: A0A267FBD6 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig009290g1 PE=4 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 1.882e-7
Identity = 32/93 (34.41%), Postives = 48/93 (51.61%), Query Frame = 1 
Query:   55 MAEFLHDLFSRITGNESF-LKCLKLCEIEDFSELIGLNESTFDQMETYIQKKCTQMPFNERSNFIGNNFAKNPDSFKFSPGIRQKILSLTKNL 330
            M +   +L  R TG  S  + CL+LC   +   L GL ++  D +E +++  C  MP  ER  ++G  FA  PD F+F  G R+ IL   + L
Sbjct:    1 MDDTCRELLGRYTGQSSAAINCLELCGYANARVLQGLTDAEIDNVERFVRDACQLMPQEERVAYVGQIFADCPDQFRFPAGTRKGILVGVQGL 93
[Close]
BLAST of SMED30000310 vs. TrEMBL
Match: I1ZID3 (Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 9.621e-6
Identity = 35/105 (33.33%), Postives = 58/105 (55.24%), Query Frame = 1 
Query:   55 MAEFLHDLFSRITGNESFLKCLKLCEIEDFSELIGLNESTFDQMETYIQKKCTQMPFNERSNFIGNN-FAKNPDSFKFSPGIRQKILSLTKNLCSVFSNESMPLN 366
            M E L +L   +T ++  +  L+LC  E   ++  LNE+    ME+YI   C+ M F+ER  +I  N F K P  FKF+P ++ ++L++   +   F N+S  +N
Sbjct:    1 MDENLKNLIQELTSSQLVINWLELCGFETLEDIEYLNENVIADMESYIGSICSSMSFDEREKYIHVNLFKKFPQQFKFTPCLKSRLLNVADAISRQF-NKSSQIN 104
[Close]
BLAST of SMED30000310 vs. Planmine SMEST
Match: SMESG000026581.1 (SMESG000026581.1)

HSP 1 Score: 82.8037 bits (203), Expect = 1.572e-16
Identity = 40/135 (29.63%), Postives = 81/135 (60.00%), Query Frame = 1 
Query:   55 MAEFLHDLFSRITGNESFLKCLKLCEIEDFSELIGLNESTFDQMETYIQKKCTQMPFNERSNFIGNNFAKNPDSFKFSPGIRQKILSLTKNLCSVFSNESMPLNSNNVKEICQRLVEEDMIKSLTLPTSAIKNVM 459
            M+  +  L S I+G++    C K+ EI + S+++ ++E T   ME +IQKKC+ +P +ERS F+ ++   NP+ F   PG+ Q+I++  + + ++F  E++P N  NV  +  +L++  +  +  +  + ++NV+
Sbjct:    1 MSNQIPKLISVISGSDKLEACFKVSEIYNVSDVMNIDEKTIQHMEKFIQKKCSNIPLSERSKFLDDSLLNNPEMFMIPPGLTQRIINNCQKVSTIF--ENIPANDKNVAIVSNKLLKNSVKSNSAINLNMLENVL 133
[Close]
BLAST of SMED30000310 vs. Planmine SMEST
Match: SMESG000026705.1 (SMESG000026705.1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.104e-14
Identity = 36/98 (36.73%), Postives = 62/98 (63.27%), Query Frame = 1 
Query:   55 MAEFLHDLFSRITGNESFLKCLKLCEIEDFSELIGLNESTFDQMETYIQKKCTQMPFNERSNFIGNNFAKNPDSFKFSPGIRQKILSLTKNLCSVFSN 348
            M++    L S I+G  +   CL  C+I + S++I +++     +ET I++KC++M  N+R  +I + F K PD FKF+PG+R++IL+  K+L  V+ N
Sbjct:    1 MSDIFIKLLSDISGAHNLEACLNKCDITNLSDIIDIDDRCLLFIETCIKEKCSKMAENDRLVYIEDVFMKRPDIFKFAPGVRERILNTVKSLKKVYKN 98
[Close]
BLAST of SMED30000310 vs. Planmine SMEST
Match: SMESG000072339.1 (SMESG000072339.1)

HSP 1 Score: 63.929 bits (154), Expect = 8.812e-11
Identity = 35/135 (25.93%), Postives = 68/135 (50.37%), Query Frame = 1 
Query:   67 LHDLFSRITGNESFLKCLKLCEIEDFSELIGLNESTFDQMETYIQKKCTQMPFNERSNFIGNNFAKNPDSFKFSPGIRQKILSLTKNLCSVFSNESMPLNSNNVKEICQRLVEEDMIK-SLTLPTSAIKNVMPIA 468
            + D  + +TG+       KLC+    ++L+  N+++ D+ME YIQ +C+ M   ERS ++  +  +NP  F  SPG+R +I      + +  +  S+ L+        Q+L+  + I         ++KN+ P++
Sbjct:    5 IFDALNYLTGSSKTSARFKLCDFNTITDLLSFNDTSIDKMEEYIQLQCSLMDLAERSIYLDGDDIQNPKCFMISPGLRNRICKAVSTIVNSMNGASLSLS--------QKLLNHNFIDYGFKDNIVSVKNIKPLS 131
[Close]
BLAST of SMED30000310 vs. Planmine SMEST
Match: SMESG000036851.1 (SMESG000036851.1)

HSP 1 Score: 61.6178 bits (148), Expect = 2.714e-10
Identity = 29/90 (32.22%), Postives = 51/90 (56.67%), Query Frame = 1 
Query:   55 MAEFLHDLFSRITGNESFLKCLKLCEIEDFSELIGLNESTFDQMETYIQKKCTQMPFNERSNFIGNNFAKNPDSFKFSPGIRQKILSLTK 324
            M EF   +   +TG+E  + CL+LC+I++  ++I +++   D++E + ++ C  M  ++   +I   F  NP  F  SPGIR K+L   K
Sbjct:    1 MDEFCKQIILEVTGSEKIIACLELCDIKEDVDVINIDDKVIDRIENFTKECCLLMLPDQMQFYIDERFYNNPSRFLISPGIRIKLLRSVK 90
[Close]
BLAST of SMED30000310 vs. Planmine SMEST
Match: SMESG000044230.1 (SMESG000044230.1)

HSP 1 Score: 60.077 bits (144), Expect = 2.676e-9
Identity = 35/105 (33.33%), Postives = 58/105 (55.24%), Query Frame = 1 
Query:   55 MAEFLHDLFSRITGNESFLKCLKLCEIEDFSELIGLNESTFDQMETYIQKKCTQMPFNERSNFIGNN-FAKNPDSFKFSPGIRQKILSLTKNLCSVFSNESMPLN 366
            M E L +L   +T ++  +  L+LC  E   ++  LNE+    ME+YI   C+ M F+ER  +I  N F K P  FKF+P ++ ++L++   +   F N+S  +N
Sbjct:    1 MDENLKNLIQELTSSQLVINWLELCGFETLEDIEYLNENVIADMESYIGSICSSMSFDEREKYIHVNLFKKFPQQFKFTPCLKSRLLNVADAISRQF-NKSSQIN 104
The following BLAST results are available for this feature:
BLAST of SMED30000310 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 SMED30000310 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 SMED30000310 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 SMED30000310 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 SMED30000310 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 SMED30000310 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 SMED30000310 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 SMED30000310 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A267F3C91.815e-734.41Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267FBD61.882e-734.41Uncharacterized protein OS=Macrostomum lignano OX=... [more]
I1ZID39.621e-633.33Uncharacterized protein OS=Schmidtea mediterranea ... [more]
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BLAST of SMED30000310 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 SMED30000310 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 SMED30000310 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 SMED30000310 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 SMED30000310 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 SMED30000310 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000026581.11.572e-1629.63SMESG000026581.1[more]
SMESG000026705.11.104e-1436.73SMESG000026705.1[more]
SMESG000072339.18.812e-1125.93SMESG000072339.1[more]
SMESG000036851.12.714e-1032.22SMESG000036851.1[more]
SMESG000044230.12.676e-933.33SMESG000044230.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000310 ID=SMED30000310|Name=SMED30000310|organism=Schmidtea mediterranea sexual|type=transcript|length=2256bp
ATTTTAAAATAAAAATTTAAATTGTTTTAAAATAATTTATGTATCTAAAA
TTTAATGGCTGAATTTTTGCATGATCTTTTTTCTAGGATAACCGGAAATG
AAAGTTTTCTAAAATGTTTAAAACTTTGTGAAATTGAGGATTTTTCAGAA
TTGATTGGACTAAATGAGTCTACATTTGACCAAATGGAGACATATATTCA
GAAAAAATGTACTCAAATGCCTTTCAATGAACGATCAAATTTTATTGGAA
ATAATTTCGCCAAAAATCCAGATAGTTTCAAGTTTTCACCAGGAATTCGA
CAGAAAATTTTGAGTCTAACTAAAAATTTATGTTCAGTTTTTTCAAATGA
GAGTATGCCGTTAAATTCGAATAATGTCAAAGAAATATGTCAAAGGCTTG
TAGAAGAAGATATGATTAAAAGTTTAACCTTGCCTACATCTGCAATAAAA
AACGTTATGCCTATTGCAAATATCCATTCACAATTGGTTCCTATCAATCA
AATGCCAAATCATATTGATCTCGATGAGCCAGTTATAACCAAAATTATTC
ATGCCAGTACAAATCAGAAACCGAGAGTATCTTGTAACAATATCTTTCAA
AGGTTGGATTTGTTTAGTAAAGAGTTAACGGTATCCGATGTAGCTGAGAA
TAATGTCCCAGTGTCGAAAGGAATGTATTTTCCATTTATTAATATTCAAC
ACAATAACGAGTCAAACAAGGAAAATTCCAACAGGAATGAAATGACTAAC
CACAAAAGAAGTCCTAAGAAAGTATTAAAACGGAAAGCTGAGAATAATGT
CCCAGTGTCGAAAGGAATGTATTTTCCATTTATTAATATTCAACACAATA
ACGAGTCAAACAAGGAAAATTCCAACAGGAATGAAATGACTAACCACAAA
AGAAGTCCTAAGAAAATATTAAAACGGAAAGCTGAAAAGGCTTCGACAAG
CAAAGAGAAAGTTGTAAATCGTTTGCAAAAATATAGAAAATTAAAGAAAA
GTCCGAATAAAGGCGCTCGTGGTGCGACTCTTGAAAGATCTAAATGGGGA
TCTGTCGAAAACCGCGTTTACAATTCGACACGATCAAGGAGCCAGAAACT
CGATCCGGAAATCATAACCAATCAACAGAAGGTTGTTACTCCGCCCAGAA
TTAAAAGAAAGTACACGAAGCGTTTAAAACCAAATCAAATAGAAGTTCCC
ACTGGAGAAAGCGGCGAAAAATTGTCAGCTCGCATTATTTCATCAGAATC
ACTGCCAGATAAAGAAAGCAATTTGATTGAAGGAAATCCTGGTGAAAATC
CAAAGGAGCCATCTAGGCCAACCGAGAAAACTATAATTAAAGTAGATGAA
ATGAATTCGAAAGTCCCTAATGTTCCCTTGACGATAATTGATATTATGGA
TACTGCGAACAAACAGGCTGTATCAGAACCTAAAGGAACAGTGCCAAAGC
AATCTATCACGTCGGAAAAAATCCCAATCAAACTGATAAGCACCAATAGT
CAATTGACCAAAGGTGTTCCACCTCCAAAATCTGTCAAAGTAATCCTACA
GCCAAATTTATCCAATGGAAACATGTCGCTGGGGATCCCATCAAGGACCA
CCGAATTAGTAACTGGCAATATGTTGACGTCTATACCAATATTTCCCCAG
TTGCCAGTCGGGTCTGTCGACAAGCCAAAGTGCCCACCGAGATTGCAATT
GTCAGATGCGCCGTTCCAGTGTTTCGATTCCAATGTCAACAAGAAAAAGC
CGACCAAGAAGTTTCCGGCAAAACTGACCAATGGTGTGCTGAATAACCCA
ATGAAACCAATTGCACAACCAAAGGTTTTGCCGGCAAATCAACCAGTCAA
GCCCAAACGGAAGAAACCACTCCCAATTAGCTATTTATTCAAAACCAGTC
CAGAAAAGCTTAAAAACAATGAAGCAGAAATAGTAAAAACTCCATCAATT
CCCGTATTCAAATTGGAACCAGTTTATGCGGATACGACCAGAACTAACCT
TTTCGAACAACTGCTGGACTCGACTATCGACCCAAACATGAATCCCCAAT
GGACGAGCACCCCATATTTCAACTCAAACAGATTTATCAACTCCGCCAAG
CACCAGAAACAGATATCATCGGAAGACTCGCGGACTGTGGACAGAGCAAA
CATTTAGAATGAGCTCTTGATTCGTGACTACCGAGATTTGTAAATATTAT
CAAGATGATGCAACCGTGACAATTGATTAGTTCGGTGTTTTCATATTTAA
TAAATG
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protein sequence of SMED30000310-orf-1

>SMED30000310-orf-1 ID=SMED30000310-orf-1|Name=SMED30000310-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=701bp
MAEFLHDLFSRITGNESFLKCLKLCEIEDFSELIGLNESTFDQMETYIQK
KCTQMPFNERSNFIGNNFAKNPDSFKFSPGIRQKILSLTKNLCSVFSNES
MPLNSNNVKEICQRLVEEDMIKSLTLPTSAIKNVMPIANIHSQLVPINQM
PNHIDLDEPVITKIIHASTNQKPRVSCNNIFQRLDLFSKELTVSDVAENN
VPVSKGMYFPFINIQHNNESNKENSNRNEMTNHKRSPKKVLKRKAENNVP
VSKGMYFPFINIQHNNESNKENSNRNEMTNHKRSPKKILKRKAEKASTSK
EKVVNRLQKYRKLKKSPNKGARGATLERSKWGSVENRVYNSTRSRSQKLD
PEIITNQQKVVTPPRIKRKYTKRLKPNQIEVPTGESGEKLSARIISSESL
PDKESNLIEGNPGENPKEPSRPTEKTIIKVDEMNSKVPNVPLTIIDIMDT
ANKQAVSEPKGTVPKQSITSEKIPIKLISTNSQLTKGVPPPKSVKVILQP
NLSNGNMSLGIPSRTTELVTGNMLTSIPIFPQLPVGSVDKPKCPPRLQLS
DAPFQCFDSNVNKKKPTKKFPAKLTNGVLNNPMKPIAQPKVLPANQPVKP
KRKKPLPISYLFKTSPEKLKNNEAEIVKTPSIPVFKLEPVYADTTRTNLF
EQLLDSTIDPNMNPQWTSTPYFNSNRFINSAKHQKQISSEDSRTVDRANI
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 216..301
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 397..422