SMED30000734

Overview
NameSMED30000734
Smed IDSMED30000734
Length (bp)2665
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 SMED30000734 (SMED30000734) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30000734 (SMED30000734) 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 SMED30000734 (SMED30000734) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30000734 (SMED30000734) 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




SMED30000734

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30000734 SmedASXL_073052SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
muscle cellSMED30000734 dd_Smed_v4_19622_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
anterior sideSMED30000734 dd_Smed_v4_19622_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
SMED30000734 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004429:38564..41230 +13020
v31.002138:40823..43520 +12936
Homology
BLAST of SMED30000734 vs. TrEMBL
Match: W4YIB3 (TTF-type domain-containing protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 1.224e-11
Identity = 43/109 (39.45%), Postives = 59/109 (54.13%), Query Frame = -1
Query: 1070 EVQEEILQLMSHIILRQLADEINKRKYFGILTKQQAAADHMPLF*EQEP*C*RN----------VFGMYILDCCDGSTFFNTIKDALQRLNVKMKNFKAACFDGASAFQ 1366
            E+QEE++ LMS  ++RQLA ++N  K F IL  Q +    M    EQ   C R           V G++ ++ CD  T F TIKD L R N+ +   +AA FDGA+ FQ
Sbjct:  322 EIQEEMIDLMSKTLMRQLAADMNG-KPFAILADQTSDVSKM----EQLCICIRTATEELAVEERVIGLHAMNKCDSETVFKTIKDVLLRYNLPLTLCRAASFDGAATFQ 425          

HSP 2 Score: 33.113 bits (74), Expect = 1.224e-11
Identity = 18/39 (46.15%), Postives = 20/39 (51.28%), Query Frame = -2
Query: 1366 QGLTL*SHEDTESNFKQLLKLRCHDSPEHLL*MTRKTTW 1482
            QGL    H D  SNF  LL LRC D       + RKT+W
Sbjct:  280 QGLPTRGHTDQNSNFVGLLNLRCKDVEGLDKWLARKTSW 318          

HSP 3 Score: 46.595 bits (109), Expect = 7.653e-8
Identity = 31/70 (44.29%), Postives = 49/70 (70.00%), Query Frame = -1
Query:  245 PASTATGERSFNHLKLLKTRILSKMFQKRLNHLLIV*IYREEVDQLDLPKLLNEFILQNEMQRK-TFAIL 451
            PA+TAT E S + L+ +KT + S M   RLN LL++ +YRE+V+ +++ +L+NEFI   + +RK T AI+
Sbjct:  704 PATTATAEHSSSTLRRVKTYLRSTMSLARLNSLLLLNVYREQVESMNITELVNEFISCGDSKRKNTLAII 773          

HSP 4 Score: 41.5874 bits (96), Expect = 7.653e-8
Identity = 24/87 (27.59%), Postives = 46/87 (52.87%), Query Frame = -3
Query:  453 PIENLLLCSFRRNSIDVDDLDLVCQQYGDKLVKIRLSTQLLGLENFRDNMKD-VELVAIAETIKQIGNSEVMSIIPLRVRLIQFYLM 710
              E+LL+ ++  N + ++ ++ V   +GD L   RL  QL  LEN ++   +    +++ + I  I  S +  +IP  V+L + YL+
Sbjct:  616 ATEDLLMSAWSSNEVPLESMECVVNHFGDNLDGPRLEAQLQVLENLKETSGEPGSNLSVDKIISAISRSGMQKMIPQVVKLCKLYLV 702          
BLAST of SMED30000734 vs. TrEMBL
Match: A0A151K420 (Dimer_Tnp_hAT domain-containing protein (Fragment) OS=Trachymyrmex cornetzi OX=471704 GN=ALC57_08606 PE=4 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 5.440e-10
Identity = 32/70 (45.71%), Postives = 50/70 (71.43%), Query Frame = -1
Query:  248 SCPASTATGERSFNHLKLLKTRILSKMFQKRLNHLLIV*IYREEVDQLDLPKLLNEFILQNEMQRKTFAI 457
            + P S+ + ERSF+ L+ LKT + + M QKRLN++ I+ IYR+    LDL  L+N+FI++N+M+  TFA+
Sbjct:   23 TIPGSSCSNERSFSALRRLKTYLRATMLQKRLNNIAILNIYRDIAQNLDLELLMNDFIIKNKMRTATFAL 92          
BLAST of SMED30000734 vs. TrEMBL
Match: H3ANJ3 (Uncharacterized protein OS=Latimeria chalumnae OX=7897 PE=4 SV=1)

HSP 1 Score: 65.4698 bits (158), Expect = 4.828e-9
Identity = 37/110 (33.64%), Postives = 60/110 (54.55%), Query Frame = -1
Query: 1070 LEVQEEILQLMSHIILRQLADEINKRKYFGILTKQQAAADHMPLF*EQEP*C*RNV----------FGMYILDCCDGSTFFNTIKDALQRLNVKMKNFKAACFDGASAFQ 1369
            + +QEEI+ L++  I   +A EI +RK FG++  + A    +    EQ     R+V           G+++LDCC+  T + T+KD L RL + + N +A C +GA+ FQ
Sbjct:  111 VPIQEEIIALIASTIQHDIAREIRERKMFGLMADETADVSRI----EQMVITVRSVEDDLEVYEELLGLHLLDCCNSKTIYKTLKDILIRLIIPLGNCRAFCAEGAATFQ 216          

HSP 2 Score: 26.9498 bits (58), Expect = 4.828e-9
Identity = 16/39 (41.03%), Postives = 21/39 (53.85%), Query Frame = -2
Query: 1366 QGLTL*SHEDTESNFKQLLKLRCHDSPEHLL*MTRKTTW 1482
            +G+    H+D  SNFKQLL L   +       +T KTTW
Sbjct:   70 KGIATYGHDDLNSNFKQLLLLMSKNDDVLRDWLTWKTTW 108          
BLAST of SMED30000734 vs. TrEMBL
Match: A0A1X7SGE1 (DUF4371 domain-containing protein OS=Amphimedon queenslandica OX=400682 PE=4 SV=1)

HSP 1 Score: 63.929 bits (154), Expect = 6.896e-9
Identity = 37/108 (34.26%), Postives = 61/108 (56.48%), Query Frame = -1
Query: 1079 EVQEEILQLMSHIILRQLADEINKRKYFGILTKQQA-AADHMPLF*EQEP*C*RNV-----------FGMYILDCCDGSTFFNTIKDALQRLNVKMKNFKAACFDGAS 1366
            E+Q EIL+LM+H ILR+++  ++   ++ ++  +   +++H     EQ   C R V            G Y +D    ST F+++KD L RLN+ ++N +A CFDGAS
Sbjct:  133 EIQNEILRLMAHSILRRISQSVHNNTHYALMADEVTDSSNH-----EQFVICLRWVDSISFAVNKDLVGFYQVDDITASTLFSSLKDVLLRLNINIQNCRAQCFDGAS 235          

HSP 2 Score: 27.7202 bits (60), Expect = 6.896e-9
Identity = 14/27 (51.85%), Postives = 14/27 (51.85%), Query Frame = -2
Query: 1402 QGLTL*SHEDTESNFKQLLKLRCHDSP 1482
            QGL L  H   E NF QLLKL     P
Sbjct:   90 QGLALRGHSSNEGNFIQLLKLLSETEP 116          
BLAST of SMED30000734 vs. TrEMBL
Match: A0A232EPV8 (Uncharacterized protein OS=Trichomalopsis sarcophagae OX=543379 GN=TSAR_011167 PE=4 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 6.967e-9
Identity = 33/69 (47.83%), Postives = 49/69 (71.01%), Query Frame = -1
Query:  245 PASTATGERSFNHLKLLKTRILSKMFQKRLNHLLIV*IYREEVDQLDLPKLLNEFILQNEMQRKTFAIL 451
            P ST T ERSF+ L+ LKT   + M Q RLNH  I+ +YR+ V+ L++  L+N+FIL+N+ ++ TFAI+
Sbjct:  517 PGSTCTNERSFSTLRFLKTYTRATMGQDRLNHYAILYVYRDRVEALNIGDLMNKFILKNQHRKNTFAII 585          
The following BLAST results are available for this feature:
BLAST of SMED30000734 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 SMED30000734 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 SMED30000734 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 SMED30000734 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 SMED30000734 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 SMED30000734 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 SMED30000734 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 SMED30000734 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
W4YIB31.224e-1139.45TTF-type domain-containing protein OS=Strongylocen... [more]
A0A151K4205.440e-1045.71Dimer_Tnp_hAT domain-containing protein (Fragment)... [more]
H3ANJ34.828e-933.64Uncharacterized protein OS=Latimeria chalumnae OX=... [more]
A0A1X7SGE16.896e-934.26DUF4371 domain-containing protein OS=Amphimedon qu... [more]
A0A232EPV86.967e-947.83Uncharacterized protein OS=Trichomalopsis sarcopha... [more]
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BLAST of SMED30000734 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 SMED30000734 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 SMED30000734 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 SMED30000734 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 SMED30000734 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 SMED30000734 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000734 ID=SMED30000734|Name=SMED30000734|organism=Schmidtea mediterranea sexual|type=transcript|length=2665bp
CGATATTTAAGGAAATATAAATGATCTTTTAAAATATATTATAACATTAA
AACCGGTGACTTAATTAACATCCATGTTAATTATTGGGGAGCAATAAATT
TAAAATAAAAGTTAAACTTTTTCCTTGAACCCGATCTCATTTTCAAATTC
AAATAAAACTTTATTTTCCATTAACCACATACAAGTTATGAAGCAACGGT
AAACTGCGAGTGCATTATTTTGTGAACTGTCAATCAATTAGTTATAAGAT
TGCAAAGGTTTTTCTCTGCATTTCATTTTGTAGAATAAATTCATTCAATA
GCTTCGGTAAGTCCAGCTGATCCACTTCCTCACGATAAATTTACACAATT
AGAAGATGGTTTAGTCGTTTTTGAAACATTTTACTCAGAATACGAGTCTT
TAGTAGCTTCAAGTGGTTGAATGATCGCTCACCGGTGGCAGTAGATGCTG
GACATGAGGTAAAACTGGATCAGTCTCACCCTTAGAGGGATTATGGACAT
CACTTCGCTGTTCCCGATCTGCTTTATGGTTTCTGCAATTGCCACTAATT
CTACGTCTTTCATATTATCACGAAAATTTTCCAAACCCAATAACTGGGTT
GATAAACGTATTTTGACCAGCTTATCGCCATATTGCTGACACACCAGATC
CAAGTCATCGACATCAATGGAGTTTCTGCGGAAACTGCACAATAGTAAAT
TTTCAATAGGAAGACTTCCACAGAAATTCCATCCGATCCTCTTTTCTGTG
TGACGATAGCCTTATCATAGCGTGACGCAGTAGCCGTAATCCATCACCAG
CTGAACAGCTTTCTGTCTGCAAACTGCTGCTCAATCTGTCAGTGATTTCG
AACAACAGGGACGCAATTTTCAGACTAATGTGCTAGTGAAATTCGAAGTC
AAAAAGCCACTGATTTATTCTCCATAATCTCCAACAGTTTTTCAATGACT
GTCAACATTTCTTGGTTGTGAGAAATTGCTCACACACCAGAGACTACAAC
AGGTGAGTTTCTTTTGGAGGAGGCTCTGAAAAATATGATCAAATCTTGAA
TGAGTTGGAAAAACTCACTTTGGAATGCAGATGCGCCATCAAAGCAGGCT
GCTTTGAAGTTTTTCATTTTCACATTCAGCCGTTGAAGTGCATCCTTGAT
AGTGTTGAAGAAGGTTGAACCATCACAGCAATCTAAGATATACATACCAA
AAACATTTCGTCAACATCAAGGTTCTTGCTCTCAGAACAAAGGCATATGG
TCAGCTGCAGCCTGCTGTTTTGTCAAAATTCCAAAATACTTTCGCTTATT
TATTTCGTCGGCTAATTGCCGAAGAATTATATGAGACATAAGTTGCAGGA
TTTCCTCTTGAACTTCCAAGTGGTTTTCCTGGTCATTCACAATAGATGTT
CTGGAGAGTCATGGCATCGAAGTTTCAGTAGCTGTTTAAAATTGCTCTCA
GTGTCTTCATGACTTCAAAGTGTCAGACCTTGGCATTTCCTTCGCAAGTT
GAGAATTTAGTTGTGACATAATGCATTCACCTTTCACTAAATTACAAAAT
TTGTAAACAGCCTAACAGCGGGCATGAGTCTTCATTTTTTCTAAACCAAT
CCGTGGCCTTCAGCCATGTTGCTAATCATTTTGTAGTGAAAGCGTCTTCA
CTCTTCGGGTTTGTAGACGTTCCTTACTAGTACACTTGCCGACATGGATG
GCAAAATGTACATTTCATTTCTGTATCCCAGTCCAGCCAAGAGAATAATT
CAAACCATACTGAGAGGAATTGACGATTGTTTTTGTCATTATTAAGAAAA
TCAACATTGTGAGGCTGCATTGGTTCCAAACGCAAAACAGGCATCATTTT
CACTTTCTTTTTTGATGAAATCAATGAGGAGACTTCTTCATTGAGATTGA
TGATATCTGTGGGGTAGGAGCCAAGAGAGATGGATTATGCATTGACGAAT
GTTTCATAGAAACAGGAATCACAGAGGAGACGTGTTTCTTGATGTTTGCT
GTTGGAGTCAAGAGGAGTAGAGTAGGCGTGGTGGAGGAATACAGTATCAT
CAGTTTTCTTCAAGAAATAATTCGGCGCATACTTGTGGTCAGTTGTAGAG
GCAAATCATGTAGTGACAATGGTCAATGAATTAGTAATGAATAACATCTT
ATGTCATATGATGCAGGAGGTGTGAGAGAGTGAGTCATTGTTTGTGTATG
TGCGCACTGTATGACTTTCACTCTCTTTGACGCAGTCCCATGCATCACAC
CATCTCACTATATAAAACGCAGACATGGTTAGTTTTAAATTGTTACTATA
TAGTTACTATATGTCGTTAGCTGGAATAGCTAACGGTTAACAATCAGTAG
AATGAATTGTCCTTGTGGTGGGTGACCAAAAAGTGTGTAGGCTGTGGATG
GTTTGAGGTTTTGAAGTATGTGAATAGTAGGTAGCTTATGTTGTATGGCT
TATACTTATTTAACATGCATTGGTCCAACAAGGATTCGACAAAAGAAAAC
TGAACAATCCTAAAATAGACGGATGGGTACACTTTAGCACTTTTTTGATG
GAGCGAAACCATATTCTTGTTCTCCAATATTCTTATTAGTGGAGCAGCTG
CTCCCTTACTCCCTTAGAATCGACGCATCTGATTAACATAATCATGATAC
CGATTTATGTATTAG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 4..26