SMED30007850

Overview
NameSMED30007850
Smed IDSMED30007850
Length (bp)2850
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 SMED30007850 (SMED30007850) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007850 (SMED30007850) 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 SMED30007850 (SMED30007850) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007850 (SMED30007850) 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




SMED30007850

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30007850h1SMcG0002949 Contig3121GPL15192PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
protonephridiaSMED30007850h1SMcG0002949 dd_Smed_v4_3418_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30007850h1SMcG0002949 dd_Smed_v4_3418_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007850h1SMcG0002949 dd_Smed_v4_3418_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30007850h1SMcG0002949 dd_Smed_v4_3418_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30007850h1SMcG0002949 dd_Smed_v4_3418_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007850h1SMcG0002949 Contig38712uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007850h1SMcG0002949 Contig38712newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007850h1SMcG0011427 Contig3121GPL15192PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30007850 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.013089:5134..10229 +10890
Homology
BLAST of SMED30007850 vs. Planmine SMEST
Match: SMESG000001248.1 (SMESG000001248.1)

HSP 1 Score: 945.266 bits (2442), Expect = 0.000e+0
Identity = 487/492 (98.98%), Postives = 490/492 (99.59%), Query Frame = 2
Query: 1076 MSTAGKEITISSNDHSPVILTXXXXXXXXXXXXXXVFKAKASKVIRSSSCLHSPKVKRAKYXXXXXXXXXXSFSSTLMTASSDIGNQSENINRKAITFLMNSRGKSEPPGDLLKDAYTDTLPNGIIKYYSWNDISNECKNQLEYEQEVPVIVNQKEFSLNLIKTKSNSSSLNEVTDICKPEIEVLLNNDINNETCSEDEVFHTTFRPIDKTDIFDENQNFLNNSFRESSYSTFLPSIGTSSLSKTVQDASTGNLPASFESKNETKTAKSLNKQKLKDDPMESLDKLIKSIQVSCEEMRATRKSFECNKSDDDQKPSETDLVNSEDSACHSEDEIVVLNNESLEGCKEVILDENCSAISCEIYKEDLKMKKKILPVLELPISQMASCHQMSLEIMAAADSISKVNSPTNLFQQTYQRMIRNPIIVSGLFAATTYTAPIWCSYIPRNICLTKIFFGTLDYLYSSEMVQAIPNHIILTGRNTVSAASKTIKRILF 2551
            MST GKEITISSNDHSPVILTAKIEKAEKHKAKIEVFKAKASKVIRSSSCLHSPKVKRAKYNVK+VINNVVSFSSTLMTASSDIGNQSENINRKA+TFLMNSRGKSEPPGDLLKDAYTDTLPNGIIKYYSWNDISNECKNQLEYEQEVPVIVNQKEFSLNLIKTKS SSSLNEVTDICKP+IEVLLNNDINNETCSEDEVFHTTFRPIDKTDIFDENQNFLNNSFRESSYSTFLPSIGTSSLSKTVQDASTGNLPASFESKNETKTAKSLNKQKLKDDPMESLDKLIKSIQVSCEEMRATRKSFECNKSDDDQKPSETDLVNSEDSACHSEDEIVVLNNESLEGCKEVILDENCSAISCEIYKEDLKMKKKILPVLELPISQMASCHQMSLEIMAAADSISKVNSPTNLFQQTYQRMIRNPIIVSGLFAATTYTAPIWCSYIPRNICLTKIFFGTLDYLYSSEMVQAIPNHIILTGRNTVSAASKTIKRILF
Sbjct:    1 MSTDGKEITISSNDHSPVILTAKIEKAEKHKAKIEVFKAKASKVIRSSSCLHSPKVKRAKYNVKDVINNVVSFSSTLMTASSDIGNQSENINRKAMTFLMNSRGKSEPPGDLLKDAYTDTLPNGIIKYYSWNDISNECKNQLEYEQEVPVIVNQKEFSLNLIKTKSKSSSLNEVTDICKPKIEVLLNNDINNETCSEDEVFHTTFRPIDKTDIFDENQNFLNNSFRESSYSTFLPSIGTSSLSKTVQDASTGNLPASFESKNETKTAKSLNKQKLKDDPMESLDKLIKSIQVSCEEMRATRKSFECNKSDDDQKPSETDLVNSEDSACHSEDEIVVLNNESLEGCKEVILDENCSAISCEIYKEDLKMKKKILPVLELPISQMASCHQMSLEIMAAADSISKVNSPTNLFQQTYQRMIRNPIIVSGLFAATTYTAPIWCSYIPRNICLTKIFFGTLDYLYSSEMVQAIPNHIILTGRNTVSAASKTIKRILF 492          
The following BLAST results are available for this feature:
BLAST of SMED30007850 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 SMED30007850 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 SMED30007850 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 SMED30007850 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 SMED30007850 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 SMED30007850 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 SMED30007850 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 SMED30007850 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 SMED30007850 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 SMED30007850 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 SMED30007850 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 SMED30007850 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 SMED30007850 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 SMED30007850 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000001248.10.000e+098.98SMESG000001248.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007850 ID=SMED30007850|Name=SMED30007850|organism=Schmidtea mediterranea sexual|type=transcript|length=2850bp
GTCGTCATTACAAATCGATCACCAATGGCTTTGCATAAATGGCATTTCAT
TCATGTTAATTAGGATTTGAGAAGTAGCATGTTTCTGCATATGAAACCCA
CAGCGGACTCAATTTAATGATTTTAGATTTTCGTAGAACCAATGATTTTC
TTTGGATTGGAATAAACTAAAATGCTTATTAAAATGCCAATGTCATAGAA
ATACAATGTCTTTAAACATCTACTTATTGATTCCGAGGAATTACATCAAA
AAATCTCACAAGTCTCATGAAGTAAATGAAGAAATTGAAAAGTCTATTTC
TGAATTACGCGAGAAAATATCCGATTGGAATTATAAATTAGACCTTGATG
ATACCGTTGGATCAGTTTACAAATTAAAATTCGATCAATTTGAAAAAAAA
TTTCTCAGAAAATCAGATTTCGTTTTTATTCTAGTTAATTCACAGTCAGA
AGATGCATTTAAAAGTTGCGTGGAAAAATTGATAAAAACTTGTAAGAATC
CTGAAAAACTAGCGAACATTGCTGTTCTCTCGTTAAGTGCTAAAGGCTTT
GAGGAGTTAAAAAATAATAGTGTTAAATTTATCTTTATTGGAAATGAAAT
GGCTGCTGACAAATTGAATAAATGGGATAAACTAGAAAATATGTTAAAAG
AAAAAATCAGTAATAACTCTGGTGAAGAAAGTCAAACCAAAACCTCACTG
TCAATTTCAATCCCAATTTCCGGACGAAAATCACCATCAAAATTTAAAAC
ATTTTTTAACAGTTTGCCATCAAAATTTGAATCAGAAAGAAGAACCTTAC
ACAGGGCACATAAAGAAGAAGTCGAAAATACATCAAGTTCTCATCAAGAT
GTCAGATTGCCGAATATCAATGTTTCAGAAATAAGTGGAACTGGAAATGA
AGGTGTCCCTCATGCTGTTGGTCTTCGTTCAAAAGTCGATTCATCAAAAC
TGTCTTTGAATTCTCTTTTTAAAAGGCGGTCAAAGAAAGCTCGTGACTCT
GGATTGAGTTTAAATAGTTCAGTTAGTACTGGCAGTGGAAGTCGAAAAAG
TGAGGTCATAATTAATAAAGAAAGCATGTCGACAGCCGGAAAGGAAATAA
CTATTTCATCAAATGACCATTCTCCAGTCATTTTAACTGCAAAAATAGAA
AAAGCCGAAAAACACAAAGCTAAAATCGAAGTATTTAAAGCTAAAGCCAG
TAAAGTGATTCGATCTTCCAGTTGCTTGCATAGTCCAAAAGTGAAACGAG
CAAAATATAATGTGAAAAATGTTATCAATAATGTTGTTAGTTTTTCCAGT
ACTCTAATGACTGCCTCTTCTGATATCGGAAATCAAAGTGAAAATATTAA
CAGAAAAGCAATTACATTTTTAATGAATAGTAGAGGCAAAAGTGAACCAC
CGGGTGACTTATTAAAAGATGCATACACAGACACTTTGCCTAATGGGATA
ATAAAGTATTATTCCTGGAATGATATTAGTAATGAATGTAAAAACCAACT
GGAATATGAGCAAGAAGTGCCAGTAATTGTCAATCAAAAGGAATTTAGTC
TAAACCTTATAAAAACTAAAAGTAATTCCAGCAGTTTAAATGAAGTAACG
GATATTTGCAAACCGGAAATAGAGGTATTGCTTAATAATGATATCAATAA
TGAAACATGCAGTGAAGATGAAGTCTTTCATACAACATTTCGACCTATTG
ATAAAACGGATATTTTTGATGAAAATCAAAACTTCTTAAACAACAGCTTC
AGAGAATCATCCTATTCCACTTTTTTACCTTCAATCGGTACGTCATCCTT
AAGTAAAACCGTACAAGACGCGTCAACGGGAAATTTACCAGCTTCATTTG
AATCTAAAAATGAAACAAAGACAGCAAAATCTTTAAACAAACAAAAGCTA
AAAGATGACCCAATGGAATCTCTCGATAAATTAATCAAAAGTATTCAAGT
AAGCTGCGAAGAAATGCGTGCAACAAGAAAATCTTTTGAATGCAATAAAA
GTGATGATGATCAAAAACCTTCTGAGACTGATTTAGTTAATTCAGAAGAT
AGTGCTTGTCATTCTGAAGATGAAATTGTTGTTTTAAACAATGAAAGTTT
AGAAGGTTGTAAAGAAGTTATTTTAGACGAAAATTGTTCAGCAATTTCTT
GTGAAATTTACAAAGAGGATTTAAAAATGAAAAAGAAAATTTTACCTGTT
TTAGAGTTACCAATTTCACAAATGGCATCATGTCACCAAATGTCGCTTGA
AATAATGGCGGCAGCTGATTCTATTTCCAAAGTTAATTCGCCAACAAATT
TATTTCAACAAACCTATCAAAGAATGATTCGAAATCCAATTATCGTATCT
GGATTATTTGCAGCTACAACCTACACAGCTCCGATATGGTGCTCATATAT
ACCGCGAAACATTTGCCTCACTAAAATATTTTTTGGCACGTTGGATTATC
TATACTCGAGCGAAATGGTTCAAGCCATTCCGAATCATATAATTCTAACG
GGACGAAACACTGTCTCAGCTGCTTCCAAAACGATAAAGCGTATTTTGTT
TTGACAGATTTATACATATATTATTCTGCATTTGAAAATGTAACCTGGCT
TGATAGAGTGATCATTAATCAGTTTCGCATAACTCTACGTTGTCAAGGTG
AATGGATATCCAACCAAATATTCTTGATCATATTTTAGAGTGCCTATCCT
TTAACTTTCAATATATCCCAAAAGTATACACACATATATTTTGATTTTTC
ATGAGATATTTTCCGATTTCTTTTGTTCAATTATTTCGATATTTTGCATG
ATTAAATCTGTGGTTTTATAATTTCGATTTTTTTCGATTTTTAGAAAGAT
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protein sequence of SMED30007850-orf-1

>SMED30007850-orf-1 ID=SMED30007850-orf-1|Name=SMED30007850-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=783bp
MSLNIYLLIPRNYIKKSHKSHEVNEEIEKSISELREKISDWNYKLDLDDT
VGSVYKLKFDQFEKKFLRKSDFVFILVNSQSEDAFKSCVEKLIKTCKNPE
KLANIAVLSLSAKGFEELKNNSVKFIFIGNEMAADKLNKWDKLENMLKEK
ISNNSGEESQTKTSLSISIPISGRKSPSKFKTFFNSLPSKFESERRTLHR
AHKEEVENTSSSHQDVRLPNINVSEISGTGNEGVPHAVGLRSKVDSSKLS
LNSLFKRRSKKARDSGLSLNSSVSTGSGSRKSEVIINKESMSTAGKEITI
SSNDHSPVILTAKIEKAEKHKAKIEVFKAKASKVIRSSSCLHSPKVKRAK
YNVKNVINNVVSFSSTLMTASSDIGNQSENINRKAITFLMNSRGKSEPPG
DLLKDAYTDTLPNGIIKYYSWNDISNECKNQLEYEQEVPVIVNQKEFSLN
LIKTKSNSSSLNEVTDICKPEIEVLLNNDINNETCSEDEVFHTTFRPIDK
TDIFDENQNFLNNSFRESSYSTFLPSIGTSSLSKTVQDASTGNLPASFES
KNETKTAKSLNKQKLKDDPMESLDKLIKSIQVSCEEMRATRKSFECNKSD
DDQKPSETDLVNSEDSACHSEDEIVVLNNESLEGCKEVILDENCSAISCE
IYKEDLKMKKKILPVLELPISQMASCHQMSLEIMAAADSISKVNSPTNLF
QQTYQRMIRNPIIVSGLFAATTYTAPIWCSYIPRNICLTKIFFGTLDYLY
SSEMVQAIPNHIILTGRNTVSAASKTIKRILF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000101muscle cell
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: 306..325