SMED30027954

Overview
NameSMED30027954
Smed IDSMED30027954
Length (bp)2462
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 SMED30027954 (SMED30027954) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027954 (SMED30027954) 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 SMED30027954 (SMED30027954) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027954 (SMED30027954) 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



SMED30027954

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
X1 cellSMED30027954 SmedASXL_077438SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30027954 vs. Planmine SMEST
Match: SMESG000054252.1 (SMESG000054252.1)

HSP 1 Score: 235.343 bits (599), Expect = 4.500e-72
Identity = 120/166 (72.29%), Postives = 135/166 (81.33%), Query Frame = -3 
Query:  817 TTLSVSNRFARRYQQAL*DRG*TISTYGTPK*P*RNANGRDMDIELPSILIKREPGRNPAREIRQKAEGELHRLEQLELRYRFLAN*QREYLANVNRDIANVCIPSSDGYMPNYGVAHDPRDPALLESDAPVHLVVPKSLLQPDIQDILEERGAEEHAYARRRLAD 1314
            TTL+V   FA RY QAL + G TISTYGTPK P R  NG + D ELPSILIKREPGRNP REIRQKAEGELHRLEQLE RYRFL   Q+E+LA +NRDIA+  IPSSD ++P YG+A+D RDPALLE DA VHLVVPKSLLQPDI+DILE++G E HAY+RRRL D
Sbjct:   25 TTLTVPTLFAGRYTQALWNLGYTISTYGTPKWPYRKTNGPEGDFELPSILIKREPGRNPTREIRQKAEGELHRLEQLEWRYRFLVKRQKEHLARINRDIASGRIPSSDMHLPAYGIAYDHRDPALLEGDALVHLVVPKSLLQPDIRDILEDQGVEAHAYSRRRLTD 190
[Close]
BLAST of SMED30027954 vs. Planmine SMEST
Match: SMESG000054252.1 (SMESG000054252.1)

HSP 1 Score: 237.654 bits (605), Expect = 4.957e-71
Identity = 120/168 (71.43%), Postives = 136/168 (80.95%), Query Frame = -3 
Query:  811 TTLSVSNRFARRYQQAL*DRG*TISTYGTPK*P*RNANGRDMDIELPSILIKREPGRNPAREIRQKAEGELHRLEQLELRYRFLAN*QREYLANVNRDIANVCIPSSDGYMPNYGVAHDPRDPALLESDAPVHLVVPKSLLQPDIQDILEERGAEEHAYARRRLADRR 1314
            TTL+V   FA RY QAL + G TISTYGTPK P R  NG + D ELPSILIKREPGRNP REIRQKAEGELHRLEQLE RYRFL   Q+E+LA +NRDIA+  IPSSD ++P YG+A+D RDPALLE DA VHLVVPKSLLQPDI+DILE++G E HAY+RRRL D +
Sbjct:   25 TTLTVPTLFAGRYTQALWNLGYTISTYGTPKWPYRKTNGPEGDFELPSILIKREPGRNPTREIRQKAEGELHRLEQLEWRYRFLVKRQKEHLARINRDIASGRIPSSDMHLPAYGIAYDHRDPALLEGDALVHLVVPKSLLQPDIRDILEDQGVEAHAYSRRRLTDNQ 192
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BLAST of SMED30027954 vs. Planmine SMEST
Match: SMESG000005968.1 (SMESG000005968.1)

HSP 1 Score: 216.083 bits (549), Expect = 7.870e-65
Identity = 110/154 (71.43%), Postives = 128/154 (83.12%), Query Frame = -3 
Query:  811 QAL*DRG*TISTYGTPK*P*RNANGRDMDIELPSILIKREPGRNPAREIRQKAEGELHRLEQLELRYRFLAN*QREYLANVNRDIANVCIPSSDGYMPNYGVAHDPRDPALLESDAPVHLVVPKSLLQPDIQDILEERGAEEHAYARRRLADRR 1272
            QAL DRG TISTYGT + P   AN    D+ELPSILIKREPGRNPAREIRQKAE ELH LEQL+ RYRFLA  Q+E+LA +NRDIA+  IPSSD Y+P+YG+A+D RDPALL++DAPVHLVVPKS +QP I+DILE+RG EEHAY+RRR  D+R
Sbjct:   62 QALRDRGYTISTYGTAEWPKHKANEFGDDVELPSILIKREPGRNPAREIRQKAENELHCLEQLDWRYRFLARRQKEHLARINRDIASGRIPSSDEYLPSYGIAYDHRDPALLKTDAPVHLVVPKSFVQPGIRDILEDRGVEEHAYSRRRFPDKR 215
[Close]
BLAST of SMED30027954 vs. Planmine SMEST
Match: SMESG000008335.1 (SMESG000008335.1)

HSP 1 Score: 226.483 bits (576), Expect = 1.598e-63
Identity = 113/166 (68.07%), Postives = 135/166 (81.33%), Query Frame = -3 
Query:  820 STTLSVSNRFARRYQQAL*DRG*TISTYGTPK*P*RNANGRDMDIELPSILIKREPGRNPAREIRQKAEGELHRLEQLELRYRFLAN*QREYLANVNRDIANVCIPSSDGYMPNYGVAHDPRDPALLESDAPVHLVVPKSLLQPDIQDILEERGAEEHAYARRRLA 1317
            STTL+V +RFA RY+QAL D+G TIST+GTP+ P R +N  D D ELPS++IKREPGRNPAREIRQ+ EG L+R EQLE +YR+LAN +R  LA +N DI N  IPSSDG++P+Y VAHDP DPALLE DAPVHLV PK LLQPDI+DILE+R  EEH Y+RRRL+
Sbjct:   98 STTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQLERKYRYLANQKRRRLARINEDITNGHIPSSDGHLPSYRVAHDPSDPALLELDAPVHLVFPKLLLQPDIKDILEDRVTEEHVYSRRRLS 263

HSP 2 Score: 51.2174 bits (121), Expect = 3.543e-6
Identity = 24/48 (50.00%), Postives = 33/48 (68.75%), Query Frame = -3 
Query:  463 HLGNSDMDTLQGIRKELKKLRQENDSFHQHCLQLSRELQRVKATCAGP 606
            +L  + M+ ++ I  E KKLR+EN+  HQ C+QLSRELQ +KAT   P
Sbjct:  269 NLAKNSMNAIKWIGSE-KKLRRENNGLHQQCIQLSRELQWIKATWVEP 315
[Close]
BLAST of SMED30027954 vs. Planmine SMEST
Match: SMESG000057450.1 (SMESG000057450.1)

HSP 1 Score: 210.69 bits (535), Expect = 5.930e-63
Identity = 108/162 (66.67%), Postives = 131/162 (80.86%), Query Frame = -3 
Query:  814 SNRFARRYQQAL*DRG*TISTYGTPK*P*RNANGRDMDIELPSILIKREPGRNPAREIRQKAEGELHRLEQLELRYRFLAN*QREYLANVNRDIANVCIPSSDGYMPNYGVAHDPRDPALLESDAPVHLVVPKSLLQPDIQDILEERGAEEHAYARRRLADR 1299
            +++   R +QAL DRG TISTYGTP+ P R  +    DIELPS+LIKRE G+NPAREIRQ+AE ELHRLEQLE RYRFLA  Q+EYLA VNRDI +  IPS DGY+P+YG+A+D RDPALLE DAP+H+VVPKSLLQP I+D+LE+RG E+HAY+RR   D+
Sbjct:   43 ADQVCSRCRQALWDRGYTISTYGTPEWPKRKTDELRDDIELPSVLIKRELGQNPAREIRQEAERELHRLEQLEWRYRFLARRQKEYLARVNRDIRSGHIPSLDGYLPSYGIAYDHRDPALLEIDAPIHIVVPKSLLQPKIRDVLEDRGVEKHAYSRRCFPDK 204
The following BLAST results are available for this feature:
BLAST of SMED30027954 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 SMED30027954 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 SMED30027954 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 SMED30027954 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 SMED30027954 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 SMED30027954 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 SMED30027954 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 SMED30027954 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 SMED30027954 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 SMED30027954 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 SMED30027954 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 SMED30027954 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 SMED30027954 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 SMED30027954 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000054252.14.500e-7272.29SMESG000054252.1[more]
SMESG000054252.14.957e-7171.43SMESG000054252.1[more]
SMESG000005968.17.870e-6571.43SMESG000005968.1[more]
SMESG000008335.11.598e-6368.07SMESG000008335.1[more]
SMESG000057450.15.930e-6366.67SMESG000057450.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027954 ID=SMED30027954|Name=SMED30027954|organism=Schmidtea mediterranea sexual|type=transcript|length=2462bp
CTACAGCTGGTTCAGCGAGCTACAGATGGGAGGCCTATGCTCTCCTCTAC
TTCAGTTTGTGCCATTACTGATCCTCGGAGAGATTATCGCATCGTCGACA
TACTCATCTTTGGAAAATAAACAAACAACAAAAGAAATGTTTTTATTTAT
TAAATACATTACACGATAGAGATAACTCCAGTCTAAATGTTGTATCTGCT
GTTTCTGTCGCATCCTTTCGGCCCTCCCTGGCCTGGCACGAGACTTCAGT
TTGTTTGGTCGATCCACTGGGATCGTCATGTTTTTATAGGTCACTTGGAC
TGGGCGAACACCAGTGGATAGGTGACTGCCCTCCCCTCTTGGTTTGCCGC
TACGGCCACTTAACCCCCGAATCTGGATCTTCTGGGCTTGATTAAGGGTT
TTCTCCTTCTGCCAACCTCTTTGAGCGGCTTCCATCTTTTGGTAGAACCG
CTTTACCTTGTACGGCCCGGCACAGGTAGCCTTTACTCGCTGTAGTTCGC
GGCTTAACTGTAGGCAATGCTGATGGAAGCTGTCGTTTTCCTGACGGAGT
TTCTTTAGTTCCTTTCTAATTCCTTGCAGCGTATCCATATCTGAATTTCC
TAAATGATAGAAACACTGATAAATCGTAACCTTACATCTCTTACAAATCA
CATTCGTCCGAATCTTTAAATATTTTCATTATTTTCGCGAACGCTGTCGG
TAGGGATTTTCGAGCTTGGTTCAAGTATAATAATTTTTGGAGAATGACAC
GGATACGAATAGAAACGAATAAATTTATTAAAACGAATCACAAAGTTCAT
CTTCCTATTTTCTCCTGTCCGCCAAGCGTCTTCGGGCATAGGCGTGCTCT
TCAGCACCTCGTTCCTCCAGTATATCCTGAATGTCCGGCTGTAACAGACT
CTTCGGGACCACCAGATGAACGGGTGCGTCGCTCTCCAGTAGGGCCGGAT
CTCGGGGATCATGGGCCACTCCGTAGTTGGGCATATACCCATCAGAACTT
GGGATACACACGTTGGCGATATCCCGATTGACATTGGCTAGGTACTCTCT
TTGTCAATTTGCTAGAAATCTGTAGCGCAATTCCAATTGTTCAAGGCGGT
GGAGCTCGCCTTCTGCTTTTTGCCTGATTTCTCGTGCTGGGTTTCTGCCT
GGCTCCCTTTTGATGAGAATGCTGGGGAGCTCGATATCCATGTCTCGTCC
ATTGGCGTTCCGTCAGGGTCATTTGGGGGTACCGTAGGTCGATATAGTCT
ATCCCCGATCTCATAACGCTTGTTGGTATCTCCGTGCAAACCTGTTTGAT
ACACTCAAGGTAGTGGAAACCTATTAATATCAATATCAATGATTTACCAA
AACGTAGCTTCTGCGCTTCTCTTGATTGTCTGTGAAGCGACTTAATAGGC
ATAAAAAAAAGTAAGCCCTTAGTCTGCCTCTGGCTGGAGGTGGGTTATGA
ACGAATTTATGGCGTTCATAGTGGATTCGTGCGCCCTATCTGTAATTTAT
TCTCACCCATCTGCCCACTCTGATTAGGTTAACTCGTGGTTTCAAACGTT
TCTACGCTACGGGATTCATTTGTTTTCAGGGCTTAGATAGTTGGGTGCAA
TGAATGCCCAATTCATTCATTTTCATAAAAGGTTTCGCCCTCGTCCGGTT
TATTTGACAATGAGTTGTTAAATCGCAGATTCCATCAAGTAGATCGTCTC
AAGTGATTTATCGGAAATCAAAAATAATCACTGCTTAATTTTCTCCAGAA
GGAAAAAGTAATAATAGCTTGTAGATACTTCTAGTCAAATATACCATTCA
TAAATATATGTCAACCACAAAATGTTTAATCAGTTGAATATGTTTAATTA
GTTACAATTGATAAAAATGTTTAGTTAGTTACCATTGATAAAGATGTTTA
AATAATTAAAATTAACTCCACGACAATAATGAGTTGAATGATGATTAAAA
ACGTTTAATTATCTTAACATGTTGGGATTAACTGAGATTATTTAATCATT
TAAACGAAGTGGGCCATCTACCAAAACGAGTCAGGATCAACAAAATGTCG
AATCATTTCTATGAATAGTTCCATAATTTCGCAACTTGTCATGTTTAACT
ATAATGAATACTCTCTTGATAACGTTAAGCTAAACGGTTTTTCACATTTT
ATTTCTCTGTTTCAGATGAAGGAAACAGTAGGGTCTAACGAAACTGGGTA
CTTCAATCCAGTGAATATTTTTCTGGTTAATTAGGAGAGTTTGTTTCGGG
CTGTAGCGAGTTCAGTTGGTAAAGTAGATCGTTCATGATAATACATTATT
TCAATTTAGGAGAATGATTGCATTTCACAGGAAATTTTACAAGCATTAAC
ATGAAATTTTTGTAATCCTAGAGGAAGGAACGAGCATATTAGCAATTTTT
TATTAATCTACCACAGGTTTCAAATGAGGCCAGTTTGATCGTACCTGCCA
GGTGATCCTCCG
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protein sequence of SMED30027954-orf-1

>SMED30027954-orf-1 ID=SMED30027954-orf-1|Name=SMED30027954-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=179bp
MDTLQGIRKELKKLRQENDSFHQHCLQLSRELQRVKATCAGPYKVKRFYQ
KMEAAQRGWQKEKTLNQAQKIQIRGLSGRSGKPRGEGSHLSTGVRPVQVT
YKNMTIPVDRPNKLKSRARPGRAERMRQKQQIQHLDWSYLYRVMYLINKN
ISFVVCLFSKDEYVDDAIISPRISNGTN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 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: 1..24