SMED30007364

Overview
NameSMED30007364
Smed IDSMED30007364
Length (bp)538
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 SMED30007364 (SMED30007364) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007364 (SMED30007364) 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




SMED30007364

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



PAGE Curations: 20

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30007364SMESG000065363.1 SMESG000043141.1 Contig18815newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364SMESG000065363.1 SMESG000043141.1 Contig18815uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364SMESG000043141.1 Contig25438newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364SMESG000043141.1 Contig25438uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364SMESG000043141.1 Contig3969newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364SMESG000043141.1 Contig3969uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364SMESG000008530.1 SMESG000008521.1 Contig3969newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364SMESG000008530.1 SMESG000008521.1 Contig3969uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364 Contig26491newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364 Contig26491uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364 Contig34918newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364 Contig22363newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364 Contig22363uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364 Contig11892newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364 Contig11892uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364 Contig25967newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007364 Contig25967uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
whole organismSMED30007364 Contig22137newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30007364 Contig22137uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
parenchymal cellSMED30007364SMESG000065363.1 SMESG000043141.1 dd_Smed_v6_1294_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30007364 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.012845:17988..18628 -2416
Homology
BLAST of SMED30007364 vs. Planmine SMEST
Match: SMESG000065363.1 (SMESG000065363.1)

HSP 1 Score: 191.815 bits (486), Expect = 5.727e-57
Identity = 108/168 (64.29%), Postives = 136/168 (80.95%), Query Frame = 1
Query:    1 LTLHPINSNNTKSDKSVKEALKDNFIECHVDLKSLPDVVPEFVYYSTSDPSLKSTMKAKITLDFQPISSAYMYWXXXXXXXXXXXXXXXXXXMRYFNKNKGETYQLEKLERRHGYNPEKEIQEQVFKPYEREDNEMPGSHDDNRN----SADAHSNDSENKYDSQHFD 492
            L L+P+ SN++  DKSVK+ALKDNF+ECHVDLKSLPDVVPEFVYYSTSDPSLKS MKA+ITLDFQPI++AY+YWVVA+IL  V+ILL+I+L++RY  +NKGETYQL+K+ER HGY+PEKE+QE++FKPYERE+++ P    DN      S  A S  S N  +   +D
Sbjct:  636 LILNPVKSNDSTRDKSVKDALKDNFLECHVDLKSLPDVVPEFVYYSTSDPSLKSKMKARITLDFQPINTAYIYWVVAVILALVIILLMIILLVRYCMRNKGETYQLDKIEREHGYDPEKEVQEEMFKPYEREEHD-PDMMSDNTGERKLSITAQSVGSANDGELDMYD 802          
BLAST of SMED30007364 vs. Planmine SMEST
Match: SMESG000003824.1 (SMESG000003824.1)

HSP 1 Score: 104.375 bits (259), Expect = 3.521e-26
Identity = 58/131 (44.27%), Postives = 94/131 (71.76%), Query Frame = 1
Query:    1 LTLHPINSNNTKSDKSVKEALKDNFIECHVDLKSLPDVVPEFVYYSTSDPSLKSTMKAKITLDFQPISSAYMYWXXXXXXXXXXXXXXXXXXMRYFNKNKGETYQLEKLERRHGYNPEKEIQEQVFKPYER 393
            L L P+ SN+TK D+ VK+AL +NFIECH+DL S   V  +F Y+S++DP LKS MKA+ITLD++     Y+YW+V  +++ V++L++++L++R   +N+ +TYQLEKLE + G++P+ E + +    + R
Sbjct:  626 LILKPVISNDTKRDEFVKKALGNNFIECHMDLVSSDRVTSDFKYFSSTDPGLKSLMKARITLDYKGKRMTYIYWIVVGVVLLVIVLIVLILLVRGCIRNRLKTYQLEKLELQRGFDPDNESRSESLVDFSR 756          
BLAST of SMED30007364 vs. Planmine SMEST
Match: SMESG000003824.1 (SMESG000003824.1)

HSP 1 Score: 104.375 bits (259), Expect = 3.766e-26
Identity = 58/131 (44.27%), Postives = 94/131 (71.76%), Query Frame = 1
Query:    1 LTLHPINSNNTKSDKSVKEALKDNFIECHVDLKSLPDVVPEFVYYSTSDPSLKSTMKAKITLDFQPISSAYMYWXXXXXXXXXXXXXXXXXXMRYFNKNKGETYQLEKLERRHGYNPEKEIQEQVFKPYER 393
            L L P+ SN+TK D+ VK+AL +NFIECH+DL S   V  +F Y+S++DP LKS MKA+ITLD++     Y+YW+V  +++ V++L++++L++R   +N+ +TYQLEKLE + G++P+ E + +    + R
Sbjct:  624 LILKPVISNDTKRDEFVKKALGNNFIECHMDLVSSDRVTSDFKYFSSTDPGLKSLMKARITLDYKGKRMTYIYWIVVGVVLLVIVLIVLILLVRGCIRNRLKTYQLEKLELQRGFDPDNESRSESLVDFSR 754          
BLAST of SMED30007364 vs. Planmine SMEST
Match: SMESG000003824.1 (SMESG000003824.1)

HSP 1 Score: 104.375 bits (259), Expect = 3.770e-26
Identity = 58/131 (44.27%), Postives = 94/131 (71.76%), Query Frame = 1
Query:    1 LTLHPINSNNTKSDKSVKEALKDNFIECHVDLKSLPDVVPEFVYYSTSDPSLKSTMKAKITLDFQPISSAYMYWXXXXXXXXXXXXXXXXXXMRYFNKNKGETYQLEKLERRHGYNPEKEIQEQVFKPYER 393
            L L P+ SN+TK D+ VK+AL +NFIECH+DL S   V  +F Y+S++DP LKS MKA+ITLD++     Y+YW+V  +++ V++L++++L++R   +N+ +TYQLEKLE + G++P+ E + +    + R
Sbjct:  629 LILKPVISNDTKRDEFVKKALGNNFIECHMDLVSSDRVTSDFKYFSSTDPGLKSLMKARITLDYKGKRMTYIYWIVVGVVLLVIVLIVLILLVRGCIRNRLKTYQLEKLELQRGFDPDNESRSESLVDFSR 759          
BLAST of SMED30007364 vs. Planmine SMEST
Match: SMESG000026407.1 (SMESG000026407.1)

HSP 1 Score: 60.077 bits (144), Expect = 8.416e-11
Identity = 55/166 (33.13%), Postives = 93/166 (56.02%), Query Frame = 1
Query:    1 LTLHPINSNNTKSDKSVKEALKDNFIECHVDL-------KSLPDVVPE-FVYYSTSDPSLKSTMKAKITLDFQP-ISSAYMYWXXXXXXXXXXXXXXXXXXMRYFNKNKGETYQLEKLERRHGYNPEKE-IQEQVFKPYERE---DNEMPGSHDDNRNSADAHSND 459
            L L+P+ SNNTK D  VK  LKD  + C V L       KS  ++  E  + Y+TS         ++I LD++P I  A   W++ +++  ++I++ I L++++  K +G++YQ+EKLE   GYN ++E I+ +  KPY R    ++  P +H +  +S D   +D
Sbjct:  656 LNLNPVISNNTKLDTMVKLMLKDTKLICRVRLLYPGSENKSEDELKQENRIIYATS-------FSSEIKLDWEPVIVEASYTWIIFLVIALILIVMFIFLLVKFTLKGQGKSYQIEKLEIAKGYNRDEELIENETIKPYLRSYTNNSSFPSNHLEKDSSKDLDYSD 814          
The following BLAST results are available for this feature:
BLAST of SMED30007364 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 SMED30007364 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 SMED30007364 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 SMED30007364 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 SMED30007364 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 SMED30007364 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 SMED30007364 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 SMED30007364 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 SMED30007364 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 SMED30007364 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 SMED30007364 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 SMED30007364 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 SMED30007364 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 SMED30007364 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000065363.15.727e-5764.29SMESG000065363.1[more]
SMESG000003824.13.521e-2644.27SMESG000003824.1[more]
SMESG000003824.13.766e-2644.27SMESG000003824.1[more]
SMESG000003824.13.770e-2644.27SMESG000003824.1[more]
SMESG000026407.18.416e-1133.13SMESG000026407.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007364 ID=SMED30007364|Name=SMED30007364|organism=Schmidtea mediterranea sexual|type=transcript|length=538bp
CTGACCCTGCATCCAATTAATTCAAACAATACCAAAAGTGATAAATCTGT
TAAAGAAGCACTCAAAGACAATTTTATAGAATGCCACGTGGATTTGAAAT
CACTTCCTGATGTCGTGCCAGAATTTGTATACTATTCCACCAGTGATCCC
TCCTTGAAATCTACAATGAAAGCTAAAATAACACTGGACTTTCAACCAAT
AAGTTCAGCATATATGTACTGGGTTGTCGCCATCATCCTGGTGTTTGTGG
TCATCTTGCTAATAATTGTACTTGTAATGCGTTATTTCAATAAAAATAAA
GGAGAAACCTACCAATTAGAGAAGCTAGAACGTCGACATGGCTATAATCC
AGAAAAAGAAATCCAAGAGCAAGTATTCAAGCCGTATGAACGAGAAGACA
ATGAAATGCCGGGGTCTCATGATGATAACAGGAATTCAGCTGATGCCCAT
AGTAATGACAGTGAGAATAAATATGATTCTCAACACTTTGATTCCAATAC
CAACCTGACAAAATGAAAAGCATTTTTGTTGATTTCCC
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protein sequence of SMED30007364-orf-1

>SMED30007364-orf-1 ID=SMED30007364-orf-1|Name=SMED30007364-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=172bp
LTLHPINSNNTKSDKSVKEALKDNFIECHVDLKSLPDVVPEFVYYSTSDP
SLKSTMKAKITLDFQPISSAYMYWVVAIILVFVVILLIIVLVMRYFNKNK
GETYQLEKLERRHGYNPEKEIQEQVFKPYEREDNEMPGSHDDNRNSADAH
SNDSENKYDSQHFDSNTNLTK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000136whole organism
PLANA:0003116parenchymal 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: 120..171
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 120..160
NoneNo IPR availableTMHMMTMhelixcoord: 70..92