SMED30003668

Overview
NameSMED30003668
Smed IDSMED30003668
Length (bp)1393
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 SMED30003668 (SMED30003668) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003668 (SMED30003668) 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 SMED30003668 (SMED30003668) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003668 (SMED30003668) 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




SMED30003668

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
zeta neoblastSMED30003668SMESG000068296.1 SMESG000068294.1 SMESG000057066.1 SMESG000057064.1 dd_Smed_v4_59927_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30003668 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001134:38198..39633 +6405
v31.002707:1552..2737 -5712
v31.003124:46055..47468 -5132
v31.007760:14261..15699 -5124
v31.003476:6565..8056 -4499
v31.005310:29489..30707 -3839
Homology
BLAST of SMED30003668 vs. Planmine SMEST
Match: SMESG000068296.1 (SMESG000068296.1)

HSP 1 Score: 363.614 bits (932), Expect = 9.786e-126
Identity = 190/195 (97.44%), Postives = 190/195 (97.44%), Query Frame = 2
Query:  551 MAQRLDIIPAHHLQTNSEGSRTNDDANTLAEPTSQPNVNRWHKPXXXXXXXQKRIVENALLQANLGGSDGTNLIGICEIMMTESTAFRNDDELNVIYARRQPGFTHSVPTMVQITITTSSHSAEVPINIHIPTSSRTTPDRDVPTSGLSLPQIISVVEPTVSRNQMASNFHQTGPNPATRSSKRRYLPVDIDGED 1135
            MAQRLDIIPAHHL TN EGSRTNDDANTLAEPTSQPNVNRWHKPNRNRRRRQKR VENALLQANLGGSDGTNLIGICEIMMTESTAFRNDDELNVIYARRQPGFTHSVPTMVQITITTSSHSAEVPINIHIPTSSR TPDRDVPTSGLSLPQIISVVEPTVSRNQMASNFHQTGPNPATR SKRRYLPVDIDGED
Sbjct:    1 MAQRLDIIPAHHLPTNLEGSRTNDDANTLAEPTSQPNVNRWHKPNRNRRRRQKRRVENALLQANLGGSDGTNLIGICEIMMTESTAFRNDDELNVIYARRQPGFTHSVPTMVQITITTSSHSAEVPINIHIPTSSRKTPDRDVPTSGLSLPQIISVVEPTVSRNQMASNFHQTGPNPATRPSKRRYLPVDIDGED 195          
BLAST of SMED30003668 vs. Planmine SMEST
Match: SMESG000057066.1 (SMESG000057066.1)

HSP 1 Score: 341.273 bits (874), Expect = 6.138e-117
Identity = 175/195 (89.74%), Postives = 181/195 (92.82%), Query Frame = 2
Query:  551 MAQRLDIIPAHHLQTNSEGSRTNDDANTLAEPTSQPNVNRWHKPXXXXXXXQKRIVENALLQANLGGSDGTNLIGICEIMMTESTAFRNDDELNVIYARRQPGFTHSVPTMVQITITTSSHSAEVPINIHIPTSSRTTPDRDVPTSGLSLPQIISVVEPTVSRNQMASNFHQTGPNPATRSSKRRYLPVDIDGED 1135
            MAQRLDI PAHH  TNSEGSRTNDDANT AEPTSQPNV+RWHKPNRNRRRRQK  V+NALLQANLGGSDGT+L+GICEIMMTESTAFRNDDELNVIYARRQP FTHSVPT+ QITITTSSHSAEVPINIHI TSSRTTPDRDVP+SG  LPQIISVVEPTVSRNQMASNFHQTG NP TR SKRRYLPVDIDGED
Sbjct:    1 MAQRLDIGPAHHFPTNSEGSRTNDDANTFAEPTSQPNVDRWHKPNRNRRRRQKHRVKNALLQANLGGSDGTDLMGICEIMMTESTAFRNDDELNVIYARRQPDFTHSVPTLAQITITTSSHSAEVPINIHISTSSRTTPDRDVPSSGRFLPQIISVVEPTVSRNQMASNFHQTGSNPTTRPSKRRYLPVDIDGED 195          
BLAST of SMED30003668 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1)

HSP 1 Score: 302.368 bits (773), Expect = 3.211e-100
Identity = 175/296 (59.12%), Postives = 213/296 (71.96%), Query Frame = 2
Query:  248 INLTRIPRIVPAPSAVAAAQYVENLERENFTLREKYNKLKGTWWSPEATKELDKKITRLSRARDDLIIENRGQRITISD*SAALRQIFTKQELQARLPSRNMAQRLDIIPAHHLQTNSEGSRTNDDANTLAEPTSQPNVNRWHKPXXXXXXXQKRIVENALLQANLGGSDGTNLIGICEIMMTESTAFRNDDELNVIYARRQPGFTHSVPTMVQITITTSSHSAEVPINIHIPTSSRTTPDRDVPTSGLSLPQIISVVEPTVSRNQMASNFHQTGPNPATRSSKRRYLPVDIDGED 1135
            +NL RIP+I PAPSAVA AQY+E LERENFTLREKYN+LK TW SPE T+E  KKI RLSRARDDLIIENR QRI IS   AA RQIFT++E QARLPSRNM QRLDIIP HHL TN +  R N++ N   + T+   VN+ H+PNRNRRRRQ+R  ENALLQ+NLG  +  +L  I E+   +  A  + ++L VI A RQP F+   P   QI IT  ++SAE+ IN+ I  +SRTTPDRD  +SG S PQIISV+EPT++R+Q + N  +   +  TR  KR+YLPVDID ED
Sbjct:    1 MNLPRIPKISPAPSAVAEAQYLEKLERENFTLREKYNRLKVTWCSPEITRERYKKINRLSRARDDLIIENRSQRIMISYECAAFRQIFTEKEKQARLPSRNMTQRLDIIPVHHLPTNPKNQRDNNNKNVPTKLTTPSTVNQRHRPNRNRRRRQRRKAENALLQSNLGVRENASLESITELFWPQPIALNDGEDLGVIDAPRQPDFSQPAPIPAQINITMDNYSAEMLINMQISIASRTTPDRDAISSGRSSPQIISVIEPTINRSQRSDNLPRAPSSSTTRPPKRKYLPVDIDEED 296          
BLAST of SMED30003668 vs. Planmine SMEST
Match: SMESG000056978.1 (SMESG000056978.1)

HSP 1 Score: 238.424 bits (607), Expect = 9.884e-77
Identity = 141/195 (72.31%), Postives = 154/195 (78.97%), Query Frame = 2
Query:  551 MAQRLDIIPAHHLQTNSEGSRTNDDANTLAEPTSQPNVNRWHKPXXXXXXXQKRIVENALLQANLGGSDGTNLIGICEIMMTESTAFRNDDELNVIYARRQPGFTHSVPTMVQITITTSSHSAEVPINIHIPTSSRTTPDRDVPTSGLSLPQIISVVEPTVSRNQMASNFHQTGPNPATRSSKRRYLPVDIDGED 1135
            MAQRLDIIPAHHL  N+E SR N++AN LAE TS  N NR HKPNRNRRRRQKR  EN LL+ANL GSDG  LI   +IM  EST FRNDDEL+VIYA RQP FTH VPT  QITI T+SHS EV INI I TSSRTT DR++P+SG S PQIISVVEP ++RNQ  SN HQTGPNPA+RS K RYLPVDIDGED
Sbjct:    1 MAQRLDIIPAHHLPANAESSRVNNEANPLAERTSYSNANRRHKPNRNRRRRQKRRAENTLLKANLRGSDGPELIEFSDIMTAESTTFRNDDELSVIYASRQPDFTHPVPTPAQITIATNSHSVEVLINIQISTSSRTTLDREIPSSGRSSPQIISVVEPRITRNQRVSNSHQTGPNPASRSPKCRYLPVDIDGED 195          
BLAST of SMED30003668 vs. Planmine SMEST
Match: SMESG000021151.1 (SMESG000021151.1)

HSP 1 Score: 231.491 bits (589), Expect = 5.674e-73
Identity = 148/295 (50.17%), Postives = 185/295 (62.71%), Query Frame = 2
Query:  248 INLTRIPRIVPAPSAVAAAQYVENLERENFTLREKYNKLKGTWWSPEATKELDKKITRLSRARDDLIIENRGQRITISD*SAALRQIFTKQELQARLPSRNMAQRLDIIPAHHLQTNSEGSRTNDDANTLAEPTSQPNVNRWHKPXXXXXXXQKRIVENALLQANLGGSDGTNLIGICEIMMTESTAFRNDDELNVIYARRQPGFTHSVPTMVQITITTSSHSAEVPINIHIPTSSRTTPDRDVPTSGLSLPQIISVVEPTVSRNQMASNFHQTGPNPATRSSKRRYLPVDIDGE 1132
            +NL  I RIV AP AVA  Q +E+LERENF +REKY K+KGTW SP+ATKEL KKIT LSR RDDL+IE R Q++TIS+ SAALRQIFT++ELQARLPSRN+AQ+++IIPAHHL TN+E    N D +T  +  S  + NR HKPNRNRR+RQ+R  EN LL ANL   +  ++  + +    E      D E  +IYA   P                       PI+I+I T+SR   + +  +SG S P II V EPT  + QMA    Q   +P  R  KRR LPVDIDG+
Sbjct:    1 MNLPSIIRIVRAPYAVAMNQRLESLERENFIIREKYEKIKGTWCSPDATKELHKKITSLSRDRDDLVIETRSQQVTISEQSAALRQIFTEKELQARLPSRNLAQQINIIPAHHLPTNAENQAINQDNSTPEDGIS--HANRRHKPNRNRRQRQRRRAENTLLLANLRSDEYPDVTEVLDSTTIERAISGYDKE--IIYAPLNPS----------------------PIHINIATTSRAMLEEEGQSSGRSSPLIILVTEPTAPQEQMAGFPQQPESHPTARCPKRRCLPVDIDGD 269          
The following BLAST results are available for this feature:
BLAST of SMED30003668 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 SMED30003668 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 SMED30003668 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 SMED30003668 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 SMED30003668 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 SMED30003668 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 SMED30003668 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 SMED30003668 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 SMED30003668 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 SMED30003668 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 SMED30003668 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 SMED30003668 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 SMED30003668 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 SMED30003668 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000068296.19.786e-12697.44SMESG000068296.1[more]
SMESG000057066.16.138e-11789.74SMESG000057066.1[more]
SMESG000046646.13.211e-10059.12SMESG000046646.1[more]
SMESG000056978.19.884e-7772.31SMESG000056978.1[more]
SMESG000021151.15.674e-7350.17SMESG000021151.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003668 ID=SMED30003668|Name=SMED30003668|organism=Schmidtea mediterranea sexual|type=transcript|length=1393bp
CCGATTGAATAAACCCTTACAGTAGACTCTCCAGACGAATCTAGCGCTTT
AGTCCGGAAAATTAATTCATCAAATGGAAAATAATAAGACTGTTTTCCAT
TTAAATCTAAGCCACGTTGCAGACGAGATTAACATACCCATCGATCGGAA
GATATTCGTTTTGTCTCAAATTATTCTTTATCACAAATTGTACATCTCAA
TTTCTCATAAAATCTTTCATCTCTAAGAACCAAATCGAGTCCATAATATA
AATCTAACCAGAATTCCAAGAATTGTTCCGGCCCCATCCGCCGTTGCTGC
GGCGCAATATGTAGAGAACCTTGAGCGGGAGAATTTCACCCTCCGCGAGA
AATATAATAAATTAAAGGGCACTTGGTGGTCTCCTGAAGCTACGAAGGAG
CTTGATAAAAAGATCACGCGGCTCTCTCGTGCCCGCGATGATCTAATTAT
CGAGAACCGAGGCCAGCGAATCACAATATCCGACTAGAGTGCCGCACTCC
GCCAAATCTTTACCAAGCAGGAACTCCAAGCTCGACTACCGAGCAGGAAT
ATGGCGCAACGCCTAGATATAATTCCGGCTCATCATTTGCAGACAAACTC
AGAGGGTTCAAGAACAAATGACGATGCCAATACGCTCGCCGAACCGACAT
CTCAGCCAAACGTGAACCGTTGGCATAAACCGAATAGAAATCGCCGTCGA
CGACAGAAGCGCATAGTCGAAAATGCACTGCTCCAAGCCAACTTAGGTGG
TAGTGATGGCACGAATTTAATAGGAATCTGCGAGATAATGATGACCGAAT
CTACAGCATTCAGAAATGATGATGAACTTAATGTCATCTACGCTCGTCGG
CAACCGGGTTTTACTCATTCCGTCCCGACCATGGTACAGATTACTATCAC
CACCAGTAGTCACTCTGCCGAGGTACCAATCAACATTCACATTCCCACCT
CATCTCGAACAACTCCCGACAGAGATGTACCTACTAGTGGGCTATCTTTG
CCGCAGATCATCTCTGTCGTTGAACCGACGGTATCGCGAAATCAAATGGC
GAGCAATTTCCATCAAACTGGTCCAAATCCAGCAACCAGGTCATCCAAAC
GCCGATACCTTCCCGTGGATATCGACGGGGAGGACTGAAGAGAAATTCAC
ATAATCGTGATAAAACTACATTCTGCTATAATAAACTGGCTGATAATTCT
TTTTTTTTGTGTAGTTGAATATTTGTGTCTGATTTGTATCTACTTTATCT
GAATATAAATTTTGCCGTTTATTGTTGTTATTTTATTCTACCCAAATTAG
CCTGCGTATTAGAAATAAAACCTTTCACGGTAAAAAGTAAATATTGAGCG
GAAAATATAAAAATTAAAATAATAACTGGTAAAATAAATGGGG
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protein sequence of SMED30003668-orf-1

>SMED30003668-orf-1 ID=SMED30003668-orf-1|Name=SMED30003668-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=196bp
MAQRLDIIPAHHLQTNSEGSRTNDDANTLAEPTSQPNVNRWHKPNRNRRR
RQKRIVENALLQANLGGSDGTNLIGICEIMMTESTAFRNDDELNVIYARR
QPGFTHSVPTMVQITITTSSHSAEVPINIHIPTSSRTTPDRDVPTSGLSL
PQIISVVEPTVSRNQMASNFHQTGPNPATRSSKRRYLPVDIDGED*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast