SMED30003528

Overview
NameSMED30003528
Smed IDSMED30003528
Length (bp)2011
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 SMED30003528 (SMED30003528) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003528 (SMED30003528) 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 SMED30003528 (SMED30003528) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003528 (SMED30003528) 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



SMED30003528

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
neoblastSMED30003528SMESG000053832.1 SMESG000051742.1 SMESG000031888.1 SMESG000017493.1 dd_Smed_v4_4474_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30003528SMESG000053832.1 SMESG000051742.1 SMESG000031888.1 SMESG000017493.1 dd_Smed_v4_4474_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
Homology
[Close]
BLAST of SMED30003528 vs. Planmine SMEST
Match: SMESG000025665.1 (SMESG000025665.1)

HSP 1 Score: 293.508 bits (750), Expect = 3.152e-94
Identity = 185/259 (71.43%), Postives = 211/259 (81.47%), Query Frame = 2 
Query:  425 KKKYQRIKGTWLSPNAAKKLYQKISRLSRAREDLIIESRSQPVLIKEQGKTLRQIFTDAEIRARIPGSTLARELNIIPVQHXXXXXXXXXXXXXXXXXXXXXQIPVVEP-XXXXXXXXXXXXXXXXXXXXXXNLLGSAEPINAPYSIQDLPPPYHEFEFPDTEADIIYAPSVVFRSPARSIHIDLVDDENEIPASNRSLERMGLDPNEIAVLTXXXXXXXXXXXXXXXSYRIDFSINENPPRYRPAKRRCFPTDIDADE 1198
            + KY+++KGT L+P+AAKKLYQKISRLSRAR+ LI+ESRSQ VLIKEQG TLRQIFTDAE+RARIPGS  AR LNIIP QHLPLE+P P+ ++PA ++ E  Q PVVEP    A RR     RRR  RRR  NL  S EPI+APYSIQDLPPPY EFEFPD EAD++YAPS  F SPARSIHI+LVDDENE P +N+SLER+GL P+EIA LTGR+P  LPLPDEPGPS R+DF+I  NPP YRPAKRRCFPTDIDADE
Sbjct:   35 QDKYRKVKGTMLTPDAAKKLYQKISRLSRARDQLIVESRSQRVLIKEQGTTLRQIFTDAELRARIPGSIWARNLNIIPAQHLPLEIPLPVHSVPASAVAEHSQTPVVEPRTGAARRRPNRNRRRRERRRRETNLFSSTEPISAPYSIQDLPPPYQEFEFPDLEADVLYAPSATFHSPARSIHINLVDDENEAPMANQSLERLGLHPSEIATLTGRVPGCLPLPDEPGPSTRVDFNITVNPPPYRPAKRRCFPTDIDADE 293
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BLAST of SMED30003528 vs. Planmine SMEST
Match: SMESG000059849.1 (SMESG000059849.1)

HSP 1 Score: 296.59 bits (758), Expect = 1.053e-89
Identity = 193/259 (74.52%), Postives = 211/259 (81.47%), Query Frame = 2 
Query:  425 KKKYQRIKGTWLSPNAAKKLYQKISRLSRAREDLIIESRSQPVLIKEQGKTLRQIFTDAEIRARIPGSTLARELNIIPVQHXXXXXXXXXXXXXXXXXXXXXQIPVVEP-XXXXXXXXXXXXXXXXXXXXXXNLLGSAEPINAPYSIQDLPPPYHEFEFPDTEADIIYAPSVVFRSPARSIHIDLVDDENEIPASNRSLERMGLDPNEIAVLTXXXXXXXXXXXXXXXSYRIDFSINENPPRYRPAKRRCFPTDIDADE 1198
            +KKYQ++KGTWLSP+AAKKLYQKISRLSR R+DLIIESR Q +LIKEQG TLRQIFTDAE+RARIPGS LAR LNIIP QHL LE PP   + P P I E  Q PV EP    A RR     RRR +RRRAA+L  + EP NAPYSIQDLPPPY EFEFPD EADIIYAP VV  SPARSIHIDLVD+ +E P  NRSLER+ LDP+EIAVLTGRLPERLPLPDEPGPS RIDF+I+ NPP YRPAKRRCFPTD+DADE
Sbjct:  520 QKKYQKVKGTWLSPDAAKKLYQKISRLSRVRDDLIIESRGQRILIKEQGTTLRQIFTDAELRARIPGSVLARNLNIIPAQHLSLETPPVTLSTPTPVIAESSQTPVAEPRSGAARRRLNRNRRRREQRRRAASLFSATEPSNAPYSIQDLPPPYQEFEFPDMEADIIYAPIVVLHSPARSIHIDLVDEVDETPTVNRSLERLMLDPDEIAVLTGRLPERLPLPDEPGPSSRIDFNIHINPPPYRPAKRRCFPTDMDADE 778
[Close]
BLAST of SMED30003528 vs. Planmine SMEST
Match: SMESG000069749.1 (SMESG000069749.1)

HSP 1 Score: 271.166 bits (692), Expect = 7.475e-86
Identity = 165/213 (77.46%), Postives = 181/213 (84.98%), Query Frame = 2 
Query:  425 KKKYQRIKGTWLSPNAAKKLYQKISRLSRAREDLIIESRSQPVLIKEQGKTLRQIFTDAEIRARIPGSTLARELNIIPVQHXXXXXXXXXXXXXXXXXXXXXQIPVVEPXX-XXXXXXXXXXXXXXXXXXXXNLLGSAEPINAPYSIQDLPPPYHEFEFPDTEADIIYAPSVVFRSPARSIHIDLVDDENEIPASNRSLERMGLDPNEIAVLT 1060
            ++KY+RIKGTWLSP AAKKLYQKISRLSRAR++LIIESRSQ VLIKEQG TLRQIFTDAE+RARIPGS LARELNIIPVQHLPLE+P PI +IPA + TE PQ  VVEP T  A RR     RRR  RRR  NLLGS EPI+APYSI DLPPPY EFEFPD EAD++YAPSVVF SPARSIHIDL+DDENE P  N+SLERMGLDP+EIA+LT
Sbjct:   35 QEKYRRIKGTWLSPEAAKKLYQKISRLSRARDELIIESRSQRVLIKEQGTTLRQIFTDAELRARIPGSVLARELNIIPVQHLPLEVPLPIHSIPASASTEHPQTTVVEPHTGAARRRPNRNRRRRERRRRETNLLGSTEPISAPYSIHDLPPPYQEFEFPDLEADVLYAPSVVFHSPARSIHIDLMDDENEAPVKNQSLERMGLDPSEIAILT 247
[Close]
BLAST of SMED30003528 vs. Planmine SMEST
Match: SMESG000028450.1 (SMESG000028450.1)

HSP 1 Score: 265.003 bits (676), Expect = 1.782e-81
Identity = 173/259 (66.80%), Postives = 200/259 (77.22%), Query Frame = 2 
Query:  425 KKKYQRIKGTWLSPNAAKKLYQKISRLSRAREDLIIESRSQPVLIKEQGKTLRQIFTDAEIRARIPGSTLARELNIIPVQHXXXXXXXXXXXXXXXXXXXXXQIPVVEP-XXXXXXXXXXXXXXXXXXXXXXNLLGSAEPINAPYSIQDLPPPYHEFEFPDTEADIIYAPSVVFRSPARSIHIDLVDDENEIPASNRSLERMGLDPNEIAVLTXXXXXXXXXXXXXXXSYRIDFSINENPPRYRPAKRRCFPTDIDADE 1198
            + KYQ++KGTWLSP+AAKKLYQKISRLSRAR++LI+ESRSQ VLIKEQG TLRQIFTDAE+RARIPGS  AR LNIIP QHLPL++P P+ ++PA + TE PQ PVVEP    A RR     RR   RRR  +LL S EPI+APYSI DLPPPYH                V F SPARSIHI+LVDDENE+P +N++L R+GLDP+EIA+LTG +P  LP PDEPGPS  +DF+IN NPP YRPAKRRCFPTDIDADE
Sbjct:  187 QDKYQKVKGTWLSPDAAKKLYQKISRLSRARDELIVESRSQRVLIKEQGTTLRQIFTDAELRARIPGSIWARNLNIIPAQHLPLDVPLPVHSVPASAGTEHPQTPVVEPRTGAARRRPNRNCRRHERRRRETHLLSSTEPISAPYSIHDLPPPYH----------------VTFHSPARSIHINLVDDENEVPVANQTLGRLGLDPSEIAILTGNVPGCLPHPDEPGPSTCVDFNINVNPPPYRPAKRRCFPTDIDADE 429
[Close]
BLAST of SMED30003528 vs. Planmine SMEST
Match: SMESG000010758.1 (SMESG000010758.1)

HSP 1 Score: 251.136 bits (640), Expect = 9.662e-78
Identity = 164/258 (63.57%), Postives = 192/258 (74.42%), Query Frame = 2 
Query:  425 KKKYQRIKGTWLSPNAAKKLYQKISRLSRAREDLIIESRSQPVLIKEQGKTLRQIFTDAEIRARIPGSTLARELNIIPVQHXXXXXXXXXXXXXXXXXXXXXQIPVVEPXXXXX-XXXXXXXXXXXXXXXXXNLLGSAEPINAPYSIQDLPPPYHEFEFPDTEADIIYAPSVVFRSPARSIHIDLVDDENEIPASNRSLERMGLDPNEIAVLTXXXXXXXXXXXXXXXSYRIDFSINENPPRYRPAKRRCFPTDIDAD 1195
            + KY R+KGTW SP A KK+YQKI+RLSRAR++LI ESRSQ VLIKEQ  TLRQ FTDAE+RAR+PGS  AR LNIIP +HLPL++P P P+ PAP   E  QIPVVEP +GAA RR     RRR  RR  AN L + EP +APY I DL PPY EFEFPD + D++YAP+V F SP RSIHI+LVDDE+E PA N +L+R+GL+  EIA L G  P   P  DEPGPS R++ SIN NP  YRPAKR+C PTDIDAD
Sbjct:   59 RNKYHRLKGTWTSPEATKKMYQKITRLSRARDELITESRSQRVLIKEQSTTLRQKFTDAELRARVPGSIWARNLNIIPEKHLPLDVPRPAPSAPAPQSIEHSQIPVVEPHSGAARRRPNRNRRRRERRRMEANFLRTTEPASAPYRIDDLSPPYQEFEFPDLDPDVLYAPTVTFHSPPRSIHINLVDDESEAPALNNALDRLGLNVGEIAALMGNAPRSPPQIDEPGPSTRVELSINVNPHPYRPAKRQCLPTDIDAD 316
The following BLAST results are available for this feature:
BLAST of SMED30003528 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 SMED30003528 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 SMED30003528 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 SMED30003528 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 SMED30003528 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 SMED30003528 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 SMED30003528 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 SMED30003528 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 SMED30003528 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 SMED30003528 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 SMED30003528 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 SMED30003528 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 SMED30003528 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 SMED30003528 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000025665.13.152e-9471.43SMESG000025665.1[more]
SMESG000059849.11.053e-8974.52SMESG000059849.1[more]
SMESG000069749.17.475e-8677.46SMESG000069749.1[more]
SMESG000028450.11.782e-8166.80SMESG000028450.1[more]
SMESG000010758.19.662e-7863.57SMESG000010758.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003528 ID=SMED30003528|Name=SMED30003528|organism=Schmidtea mediterranea sexual|type=transcript|length=2011bp
TCCCTCACCATTAATATCATCCTTACTAACTTATCTTTATTCCTACGACG
ATCACCATGACTATTATTAATAGTCACATGACTAGCTTATCGTTATTATT
ATTAGTATTGTTACTGATATTATCATTATCGTCCGTAGTACTACTAACAT
TATCGGTGACTTCAACCGTACAATTACCAACGATAAAATCGCTACTATTA
TTATTAATATAAATGCCAGTGTAACTAGAAATCTTCCACCCCTGTTTTCC
CTGACAGTGTATGACTTTTATTGAACTAAAACATACTCGACCAATCTTCT
TATTTCATTCACCTTATCTAGATGTCTAGTTTTAAAAATCTTCTGAGGAT
TCCGCGCCTGTTTCCATCGATTGTCGTTACCAGGCAGCGATTAGAAGAAC
TGGAACGAGAACATACGACTCTGAAAGAAAAAATACCAAAGGATCAAAGG
AACTTGGCTATCACCCAACGCTGCCAAGAAATTATATCAAAAGATCTCTC
GCCTGTCTCGGGCAAGAGAGGATTTAATCATTGAATCTCGCAGTCAGCCA
GTCCTGATAAAGGAGCAGGGGAAAACGCTCCGTCAGATTTTCACCGACGC
CGAGATCCGGGCTCGCATTCCGGGAAGCACCCTGGCTCGGGAGTTAAATA
TTATTCCGGTACAGCATCTCCCCCTGGAGATGCCCCCGCCAATACCTACA
ATACCAGCTCCTTCCATCACCGAACCCCCTCAAATCCCCGTGGTCGAACC
ACGCACCGGAGCAGCCAGACGACGGCCAAATCGCAGCCGTCGCCGTCGAG
AACGTCGTAGAGCCGCAAATCTCCTCGGTTCGGCGGAGCCAATTAATGCT
CCTTACTCGATACAGGACCTGCCGCCCCCGTATCATGAATTCGAGTTCCC
TGATACTGAAGCAGACATAATATATGCCCCCAGTGTCGTTTTCCGCTCAC
CAGCCAGGTCCATTCACATAGACTTAGTGGATGATGAAAACGAGATTCCG
GCATCAAATCGATCTCTAGAACGGATGGGCCTCGATCCCAATGAAATCGC
GGTCCTAACGGGCAGGTTACCGGAACGCTTGCCTCTCCCGGACGAACCAG
GACCTTCTTACCGAATTGATTTCAGTATCAACGAAAATCCTCCTCGGTAT
CGACCAGCGAAACGTCGGTGTTTCCCAACAGACATCGATGCGGACGAGTA
AAGCCAGGATCTACTGAATCAGCCGCATCATCGCATAAACTCCTTGAACT
ATATCATCAGAGTGGCGACCTTCGTCGTGTGTCCACAGAACCACAGTGTG
CAATCATCTTTCATTTTAATTTAGCTTATGTCTTAGTTATCTTTTATGTT
TTTGTAGTAGTTTTACCGTATCAATAAATCTTCAAGTTTCGGATTTCATT
TCATTTTCGTTTCTTAACTGTAAATGTTGTTAATTGATATTAGTAAGTTA
TTAGCCATAATCCGGAGAAGGGGTTGTAAAGGATAGTATTATGCGGAGGT
CAGAAGGGAATCATAAAGAGAACTCTCACGATTGTCGACTCCGTAGAAAG
GAAAACCCAAGGTTTACTGAGGCTATGAACTCTAGAGTAAAATGCATTAG
ACCTTCTATCGGCAGCAATTGACTGGGAAACGAAGGTCCTTCGAGGAGTA
TCAATAGCAATAGCGCTCACCTGCTCGTATGGCATTCGGCTGTTGCGTAC
AGTACCAACATGATTTCGGTCATGGGTACGCAATGGTTATTAAAATCATG
CGACGTATCGGGTAAATATCCCTAGCAGTTAAAAGCAAAGGCCATATCAG
TGAAATGAGTAACACCGTAATCCAAAAACTCCTATACGTCCAACAAGACA
TTGCCGCGCTGGCCAAACAAATTAAGGGTTCGCGTAAGTTTTTGCCCAAC
ACTATTATTCTAATTCTAAGGTTGGATCATTCTATATAATAATAATCTTC
ACCATTATCATAGTCTTCACCAAAAGCATCCCAATCCCCGCTATTCAAAC
TGATCTTCATA
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protein sequence of SMED30003528-orf-1

>SMED30003528-orf-1 ID=SMED30003528-orf-1|Name=SMED30003528-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=174bp
MPPPIPTIPAPSITEPPQIPVVEPRTGAARRRPNRSRRRRERRRAANLLG
SAEPINAPYSIQDLPPPYHEFEFPDTEADIIYAPSVVFRSPARSIHIDLV
DDENEIPASNRSLERMGLDPNEIAVLTGRLPERLPLPDEPGPSYRIDFSI
NENPPRYRPAKRRCFPTDIDADE*
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