SMED30001043

Overview
NameSMED30001043
Smed IDSMED30001043
Length (bp)500
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 SMED30001043 (SMED30001043) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001043 (SMED30001043) 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.
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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




SMED30001043

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30001043 SmedASXL_007088SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30001043 dd_Smed_v4_372_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30001043 dd_Smed_v4_372_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001043 dd_Smed_v4_372_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30001043 dd_Smed_v4_372_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30001043 dd_Smed_v4_372_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30001043 dd_Smed_v4_372_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30001043 dd_Smed_v4_372_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30001043 dd_Smed_v6_372_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30001043 dd_Smed_v6_372_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
SMED30001043 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.031817:4315..5703 +1151
Homology
BLAST of SMED30001043 vs. Planmine SMEST
Match: SMESG000036225.1 (SMESG000036225.1)

HSP 1 Score: 203.756 bits (517), Expect = 1.589e-68
Identity = 107/111 (96.40%), Postives = 109/111 (98.20%), Query Frame = 2
Query:   26 MKGIIQLIVLLTAFSIVSSFENLDDFEDEFHNQEKRKVKEEDTDEEGKYQEKREFKEEDTNEERKVFLEKIIDDAVESDAKEYENEIDSKNKEESKGTNDEGVNESEIAFW 358
            MKGIIQLIVLLTAFSIVSSFENLDDFEDEFHNQEKRKVKEEDTDEEGKYQEKREFKEEDT+EERKV LE+IIDDAVESDAKEYENEIDSKNKEESKGTNDEG NESEIAFW
Sbjct:    1 MKGIIQLIVLLTAFSIVSSFENLDDFEDEFHNQEKRKVKEEDTDEEGKYQEKREFKEEDTDEERKVNLEEIIDDAVESDAKEYENEIDSKNKEESKGTNDEGENESEIAFW 111          
The following BLAST results are available for this feature:
BLAST of SMED30001043 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 SMED30001043 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 SMED30001043 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 SMED30001043 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 SMED30001043 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 SMED30001043 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 SMED30001043 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 SMED30001043 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 SMED30001043 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 SMED30001043 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 SMED30001043 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 SMED30001043 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 SMED30001043 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 SMED30001043 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000036225.11.589e-6896.40SMESG000036225.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001043 ID=SMED30001043|Name=SMED30001043|organism=Schmidtea mediterranea sexual|type=transcript|length=500bp
AAAATTGTGGTTTTGAAACATAAAAATGAAAGGAATAATCCAACTTATCG
TTTTGCTGACAGCTTTTTCCATTGTCTCGTCATTTGAAAATCTTGATGAT
TTCGAAGACGAATTTCATAATCAAGAAAAACGAAAAGTTAAGGAAGAAGA
TACGGATGAAGAAGGAAAATATCAAGAAAAACGAGAATTTAAGGAAGAAG
ATACGAATGAAGAAAGAAAAGTCTTTTTGGAGAAAATAATCGATGATGCT
GTCGAGAGTGATGCGAAAGAATATGAAAATGAAATCGATTCGAAGAACAA
AGAAGAATCTAAAGGCACAAATGATGAAGGTGTAAATGAATCTGAAATCG
CGTTTTGGTGAAATTTATTTTCTTCAACTTAACTGATGAAATTAAAAATT
TGTCGTTTTTAGAATTGAAGTACATTCGAAATGTTTTAGACATGTCTAAA
ATAATTATATATGTAATTCTAGATATCATTTAACACCATGTGCTAATATA
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protein sequence of SMED30001043-orf-1

>SMED30001043-orf-1 ID=SMED30001043-orf-1|Name=SMED30001043-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=112bp
MKGIIQLIVLLTAFSIVSSFENLDDFEDEFHNQEKRKVKEEDTDEEGKYQ
EKREFKEEDTNEERKVFLEKIIDDAVESDAKEYENEIDSKNKEESKGTND
EGVNESEIAFW*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000418head
PLANA:0000420parapharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 23..43
NoneNo IPR availableCOILSCoilCoilcoord: 73..93
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 82..103
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 34..111
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 34..74
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.838