SMED30005429

Overview
NameSMED30005429
Smed IDSMED30005429
Length (bp)913
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 SMED30005429 (SMED30005429) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005429 (SMED30005429) 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 SMED30005429 (SMED30005429) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005429 (SMED30005429) 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



SMED30005429

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30005429SMESG000030956.1 SMESG000030911.1 dd_Smed_v4_902_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30005429SMESG000030956.1 SMESG000030911.1 dd_Smed_v4_902_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30005429SMESG000030956.1 SMESG000030911.1 dd_Smed_v4_902_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005429SMESG000030956.1 SMESG000030911.1 Contig30104newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005429SMESG000030956.1 SMESG000030911.1 Contig30104uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005429SMESG000030956.1 SMESG000030911.1 Contig43971newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Category 3 cellSMED30005429SMESG000030956.1 SMESG000030911.1 dd_Smed_v6_902_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30005429SMESG000030956.1 SMESG000030911.1 dd_Smed_v4_902_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
SMED30005429 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014507:11881..12663 +2680
v31.005262:2261..3043 -2662
Homology
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BLAST of SMED30005429 vs. Planmine SMEST
Match: SMESG000030911.1 (SMESG000030911.1)

HSP 1 Score: 149.828 bits (377), Expect = 1.229e-45
Identity = 92/92 (100.00%), Postives = 92/92 (100.00%), Query Frame = 1 
Query:  196 MIWTNIFLISLFILNCYTAPTNSDDVSTKXXXXXXXXXXXXXXXXXTKQTRCKAIKQTCPEKYKDCKHCLFRRKNTESGCEETGDVTCITVE 471
            MIWTNIFLISLFILNCYTAPTNSDDVSTKEFIINNFNENDIIRNDNTKQTRCKAIKQTCPEKYKDCKHCLFRRKNTESGCEETGDVTCITVE
Sbjct:    1 MIWTNIFLISLFILNCYTAPTNSDDVSTKEFIINNFNENDIIRNDNTKQTRCKAIKQTCPEKYKDCKHCLFRRKNTESGCEETGDVTCITVE 92
[Close]
BLAST of SMED30005429 vs. Planmine SMEST
Match: SMESG000030956.1 (SMESG000030956.1)

HSP 1 Score: 144.821 bits (364), Expect = 1.069e-43
Identity = 90/92 (97.83%), Postives = 90/92 (97.83%), Query Frame = 1 
Query:  196 MIWTNIFLISLFILNCYTAPTNSDDVSTKXXXXXXXXXXXXXXXXXTKQTRCKAIKQTCPEKYKDCKHCLFRRKNTESGCEETGDVTCITVE 471
            MI TNIFLISLFILNCYTAPTNSDDVSTKEFIINNFNENDIIRND TKQTRCKAIKQTCPEKYKDCKHCLFRRKNTESGCEETGDVTCITVE
Sbjct:    1 MICTNIFLISLFILNCYTAPTNSDDVSTKEFIINNFNENDIIRNDKTKQTRCKAIKQTCPEKYKDCKHCLFRRKNTESGCEETGDVTCITVE 92
The following BLAST results are available for this feature:
BLAST of SMED30005429 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 SMED30005429 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 SMED30005429 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 SMED30005429 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 SMED30005429 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 SMED30005429 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 SMED30005429 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 SMED30005429 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 SMED30005429 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 SMED30005429 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 SMED30005429 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 SMED30005429 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 SMED30005429 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 SMED30005429 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000030911.11.229e-45100.00SMESG000030911.1[more]
SMESG000030956.11.069e-4397.83SMESG000030956.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005429 ID=SMED30005429|Name=SMED30005429|organism=Schmidtea mediterranea sexual|type=transcript|length=913bp
AAAATTTCACTGCTCCATAAGCGGTAGCATAAATTTGTTTTCTAACAGAC
AAATGAACATTCTGAAACAATTTTCATTTCTAAACGCTTTGATTCTCGCA
AATTACGGTGAACAAAATATTCCTGCCTACGCCACCGACTGCAGAACGGT
TCGATATTAATAGAAATATCAGTGGTTATCAATCAAATTTCAAATATGAT
TTGGACCAACATTTTCCTTATATCTCTATTTATTTTAAATTGCTACACAG
CTCCAACAAACTCAGATGATGTGAGCACGAAAGAATTCATTATAAACAAT
TTCAACGAAAATGATATCATTAGGAATGATAATACAAAGCAAACTCGTTG
CAAAGCAATAAAACAGACTTGTCCAGAGAAATATAAAGATTGCAAACACT
GCTTATTTCGAAGAAAAAATACCGAATCTGGTTGTGAGGAAACTGGAGAT
GTAACTTGTATCACAGTAGAATAATACAAGCAAAGAAAAGAATAATTTTA
GTTCAATATAAGAAATAAATTTAAGATTTNNNANANNNNANNNCAGATGT
TGAATAGTGAAATAACCCCTTATCTGGCAGAAGATGCAGTTGTGATAAAA
TTAATATTGCGTATATATAGGATCAATAGCAGTTACAGATAGTGGCATTG
GATTTGTGAGCTTCAAACGTTATTCCATGTGTCAAATAATGAAGTCGGAC
TTATAAATGTTTAGTACTGCATACCAAAGTCTCAATATGAGAATATAATC
GGGAGTGGTTATCGTATCTTCCGCATAAAATATCCCCCAGGAGAGCTTGA
CTCATCATTTTGTTCAATGTACGTTTCTTCATCCATGATTACGAAAGGAA
ACTTTTGATTGATTGTCATTAGAAACTCTTGGTAAAATGGATTCCAAATT
TGTTCGAACAAAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..23
score: 0.813