SMED30003685

Overview
NameSMED30003685
Smed IDSMED30003685
Length (bp)724
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 SMED30003685 (SMED30003685) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003685 (SMED30003685) 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 SMED30003685 (SMED30003685) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003685 (SMED30003685) 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



SMED30003685

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymaSMED30003685SMESG000047799.1 dd_Smed_v4_23695_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
SMED30003685 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.012180:8261..8984 -3431
v31.005332:41551..42418 -2775
Homology
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BLAST of SMED30003685 vs. Planmine SMEST
Match: SMESG000047799.1 (SMESG000047799.1)

HSP 1 Score: 427.943 bits (1099), Expect = 6.647e-148
Identity = 209/227 (92.07%), Postives = 219/227 (96.48%), Query Frame = 2 
Query:   44 MPSSRAASPANSINDQDSPKPLNVQNTQNSSSRSSFAHKKNLRQISATNRITRVPSFSLINRQTEPNTSNSHNQSTTDLTNIYFMPTNYNQNQQHSPLPEIQKTLWNPTFSPKDQDFRLPIDRNNSAICKNSDINSDRNPGRGTRQKKIGIDRDIIKSADHSLNRNNEPCLKELEKINGRSQPDFEYQINGNQCKNCAESKTQLEKKKTRVKRQIEKINQLESELKE 724
            MPSSRAASPANSINDQ+SPKPLNVQNTQNSSSRSSFAHKKNLRQISATN+ITRVPSFSLINRQTE NTSNSHNQSTTDLTNIYFMPTNYNQNQQ++PLPEIQKTLWNPTFSPKDQ+FRLPIDRNNSA  +NSDINSDRNPGRGTRQK+I IDR IIKSADHS+NRNNE  LKE EK+NGRSQPDFE+QINGNQCKNCAESKTQLEKKKTRVKRQIEKINQLESELKE
Sbjct:    1 MPSSRAASPANSINDQNSPKPLNVQNTQNSSSRSSFAHKKNLRQISATNKITRVPSFSLINRQTEHNTSNSHNQSTTDLTNIYFMPTNYNQNQQYTPLPEIQKTLWNPTFSPKDQNFRLPIDRNNSATWQNSDINSDRNPGRGTRQKQICIDRQIIKSADHSMNRNNESWLKESEKLNGRSQPDFEHQINGNQCKNCAESKTQLEKKKTRVKRQIEKINQLESELKE 227
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BLAST of SMED30003685 vs. Planmine SMEST
Match: SMESG000038528.1 (SMESG000038528.1)

HSP 1 Score: 295.819 bits (756), Expect = 3.105e-94
Identity = 157/187 (83.96%), Postives = 163/187 (87.17%), Query Frame = 2 
Query:   44 MPSSRAASPANSINDQDSPKPLNVQNTQNSSSRSSFAHKKNLRQISATNRITRVPSFSLINRQTEPNTSNSHNQSTTDLTNIYFMPTNYNQNQQHSPLPEIQKTLWNPTFSPKDQDFRLPIDRNNSAICKNSDINSDRNPGRGTRQKKIGIDRDIIKSAD-HSLNRNNEPCLKELEKINGRSQPDFE 601
            MPSSRAASPANSINDQDSPKPLNVQNTQNSSSRSS AH +N RQISATNR TRVPS SL NR TE N SNSHNQSTTDLTNI FMPT YNQNQQ++PLPEIQK L NPTFSPKDQ FRL IDRNNSA  +NSDINSDRNPGRGTRQK+IG DR IIKSAD HSLNRNNE  LKE EKING+SQ DFE
Sbjct:    1 MPSSRAASPANSINDQDSPKPLNVQNTQNSSSRSSSAHNRNRRQISATNRRTRVPSLSLRNRLTESNASNSHNQSTTDLTNINFMPTRYNQNQQYTPLPEIQKNLLNPTFSPKDQKFRLSIDRNNSATWQNSDINSDRNPGRGTRQKQIGKDRAIIKSADHHSLNRNNESWLKESEKINGKSQRDFE 187

HSP 2 Score: 78.1814 bits (191), Expect = 2.515e-16
Identity = 66/181 (36.46%), Postives = 97/181 (53.59%), Query Frame = 2 
Query:  161 KNLRQISATNRITRVPSFSLINRQTEPNTSNSHNQSTTDLTNIYFMPTNYNQNQQ-HSPLPEIQKTLWNPTFSPKDQDFRLPIDRNNSAICKNSDINSDRNPGRGTRQKKIGIDRDIIK-SADHSLNRNNEPCLKELEKINGRSQPDFEYQINGNQCKNCAESKTQLEKKKTRVKRQIEKI 697
            +NL+QISA+N  T    FS IN   E N  N H QST D T++   P  Y+QNQ  HSP      + ++PT  P+   +   I++  SA+ ++  IN            ++  D D  K   +HS  RN+     +LE  N      +E+QIN +QC NCAES  QL+ +K+RVK++IE++
Sbjct:  192 ENLKQISASNSKTIDLGFSSINFPNEINVWNCHKQSTNDFTDVNGKPITYDQNQHTHSP------SQYSPT--PETNQYLAQINQLQSALKESKGINL-----------RLQQDFDDCKVKLNHSQRRNS-----QLESANK-----YEHQINRDQCANCAESTRQLQNQKSRVKKKIEEL 343
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BLAST of SMED30003685 vs. Planmine SMEST
Match: SMESG000038520.1 (SMESG000038520.1)

HSP 1 Score: 62.003 bits (149), Expect = 5.514e-11
Identity = 48/109 (44.04%), Postives = 54/109 (49.54%), Query Frame = 2 
Query:   44 MPSSRAASPANSINDQDS-----------PKPLNVQNTQNSSSRSSFAHKKNLRQISATNRITRVPSFSLINRQTEPNTSNSHNQSTTDLTNIYFMPTNYNQNQQ-HSP 334
            M   RA+    S N + S           P PL  Q  QNS SRSS AH KN RQISA+N  T    FS IN   E N  NSH  ST   T++   P  Y+QNQ  HSP
Sbjct:    1 MSFGRASRQVASYNHESSSKFHDILPNKNPFPL-TQYKQNSLSRSSSAHNKNRRQISASNSKTIDLGFSSINSLNEINVWNSHKHSTNHFTDLNGKPITYDQNQHTHSP 108
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BLAST of SMED30003685 vs. Planmine SMEST
Match: SMESG000036060.1 (SMESG000036060.1)

HSP 1 Score: 59.3066 bits (142), Expect = 5.192e-10
Identity = 44/96 (45.83%), Postives = 54/96 (56.25%), Query Frame = 2 
Query:   50 SSRAASPANSINDQDSPKPLNVQNTQNSSSRSSFAHKKNLRQISATNRITRVPSFSLINRQTEPNTSNSHNQSTTDLTNIYFMPTNYNQNQQ-HSP 334
            +SR  + +++I  + +  PL  Q  QNS SRSS AH KN RQISA+N  T    FS IN   E N  NSH  ST   T++   P  Y QNQ  HSP
Sbjct:    6 ASRQVTSSSNILPRKNQFPL-TQYKQNSLSRSSSAHNKNRRQISASNSKTIDLGFSSINSPNENNVWNSHKHSTNHFTDLNGKPIAYYQNQHTHSP 100
[Close]
BLAST of SMED30003685 vs. Planmine SMEST
Match: SMESG000038532.1 (SMESG000038532.1)

HSP 1 Score: 57.7658 bits (138), Expect = 1.988e-9
Identity = 39/80 (48.75%), Postives = 48/80 (60.00%), Query Frame = 2 
Query:   50 SSRAASPANSINDQDSPKPLNVQNTQNSSSRSSFAHKKNLRQISATNRITRVPSFSLINRQTEPNTSNSHNQSTTDLTNI 289
            +SR  + +++I    +  PL  Q  QNS SRSS AH KN RQISA+N  T VPSFS IN   E N  NSH  ST   T++
Sbjct:    6 ASRQVTSSSNILPSKNQFPL-TQYKQNSLSRSSSAHNKNRRQISASNSKTIVPSFSSINSPNEINVWNSHKHSTNHFTDL 84
The following BLAST results are available for this feature:
BLAST of SMED30003685 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 SMED30003685 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 SMED30003685 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 SMED30003685 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 SMED30003685 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 SMED30003685 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 SMED30003685 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 SMED30003685 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 SMED30003685 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 SMED30003685 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 SMED30003685 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 SMED30003685 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 SMED30003685 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 SMED30003685 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000047799.16.647e-14892.07SMESG000047799.1[more]
SMESG000038528.13.105e-9483.96SMESG000038528.1[more]
SMESG000038520.15.514e-1144.04SMESG000038520.1[more]
SMESG000036060.15.192e-1045.83SMESG000036060.1[more]
SMESG000038532.11.988e-948.75SMESG000038532.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003685 ID=SMED30003685|Name=SMED30003685|organism=Schmidtea mediterranea sexual|type=transcript|length=724bp
TTCGTATCATAATTTGAAGTTATTATCACAGCTATACGATTAAATGCCAT
CCAGTAGAGCTGCATCACCTGCAAACTCAATTAATGATCAAGATTCACCT
AAACCTCTTAATGTTCAGAACACGCAAAATTCATCATCAAGATCTTCATT
TGCACATAAAAAAAATTTAAGACAAATCAGTGCTACTAACAGAATAACTA
GAGTTCCTAGCTTCTCATTGATAAATCGTCAAACTGAACCTAATACAAGC
AATTCTCATAATCAGTCCACCACTGATTTAACTAATATTTATTTTATGCC
GACTAATTATAATCAGAATCAACAACATTCACCTCTACCAGAAATTCAAA
AAACTCTTTGGAATCCTACATTTTCGCCAAAAGATCAAGATTTCCGTTTA
CCTATTGACAGAAATAATAGCGCGATTTGTAAAAATAGTGATATAAATTC
TGATAGGAATCCTGGCCGAGGGACTAGACAGAAGAAAATCGGCATAGATC
GTGATATAATCAAATCAGCTGATCATTCATTGAATCGAAATAACGAACCT
TGCTTGAAGGAATTAGAAAAAATAAATGGAAGATCGCAGCCAGATTTTGA
ATATCAAATAAACGGAAATCAATGTAAAAATTGTGCAGAATCGAAAACAC
AGTTGGAAAAGAAAAAAACGAGAGTTAAAAGACAAATTGAAAAAATTAAC
CAATTGGAATCAGAATTGAAGGAA
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protein sequence of SMED30003685-orf-1

>SMED30003685-orf-1 ID=SMED30003685-orf-1|Name=SMED30003685-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=227bp
MPSSRAASPANSINDQDSPKPLNVQNTQNSSSRSSFAHKKNLRQISATNR
ITRVPSFSLINRQTEPNTSNSHNQSTTDLTNIYFMPTNYNQNQQHSPLPE
IQKTLWNPTFSPKDQDFRLPIDRNNSAICKNSDINSDRNPGRGTRQKKIG
IDRDIIKSADHSLNRNNEPCLKELEKINGRSQPDFEYQINGNQCKNCAES
KTQLEKKKTRVKRQIEKINQLESELKE
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 201..224
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 124..143
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 124..146
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..49