SMED30023112

Overview
NameSMED30023112
Smed IDSMED30023112
Length (bp)205
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30023112

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30023112SMESG000047804.1 SMESG000038532.1 SMESG000038520.1 SMESG000036102.1 SMESG000036067.1 SMESG000036060.1 Contig7058newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30023112SMESG000047804.1 SMESG000038532.1 SMESG000038520.1 SMESG000036102.1 SMESG000036067.1 SMESG000036060.1 Contig7058uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30023112SMESG000047804.1 SMESG000038532.1 SMESG000038520.1 SMESG000036112.1 SMESG000036060.1 dd_Smed_v4_4251_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30023112SMESG000047804.1 SMESG000038532.1 SMESG000038520.1 SMESG000036112.1 SMESG000036060.1 dd_Smed_v4_4251_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023112SMESG000047804.1 SMESG000038532.1 SMESG000038520.1 SMESG000036112.1 SMESG000036060.1 dd_Smed_v4_4251_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023112SMESG000047804.1 SMESG000038532.1 SMESG000038520.1 SMESG000036112.1 SMESG000036060.1 dd_Smed_v4_4251_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30023112SMESG000047804.1 SMESG000038532.1 SMESG000038520.1 SMESG000036112.1 SMESG000036060.1 dd_Smed_v4_4251_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymal cellSMED30023112SMESG000047804.1 SMESG000038532.1 SMESG000038520.1 SMESG000036112.1 SMESG000036060.1 dd_Smed_v4_4251_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023112SMESG000054716.1 SMESG000047804.1 SMESG000038519.1 SMESG000036102.1 Contig10395newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023112SMESG000054716.1 SMESG000047804.1 SMESG000038519.1 SMESG000036102.1 Contig10395uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30023112SMESG000047804.1 SMESG000038532.1 SMESG000038520.1 SMESG000036112.1 SMESG000036060.1 dd_Smed_v4_4251_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
SMED30023112 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009145:32263..32467 -1016
v31.002942:67221..67425 +1016
v31.017690:7779..7983 -980
v31.015478:9060..9264 +980
v31.010883:16592..16796 +971
v31.015331:8014..8218 -953
Homology
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BLAST of SMED30023112 vs. Planmine SMEST
Match: SMESG000038532.1 (SMESG000038532.1)

HSP 1 Score: 111.309 bits (277), Expect = 2.184e-30
Identity = 67/68 (98.53%), Postives = 67/68 (98.53%), Query Frame = -2 
Query:    1 RQNSRSHRDNYFSTNSADIYGTMPKWNDDYQSRNRDLHSELDRHXXXXXXXXXXXEDLRIRSNKSERK 204
            RQNSRSHRDNYFSTNSADIYGTMPKWNDDYQSRNRD HSELDRHERGIERFGEEIEDLRIRSNKSERK
Sbjct:  128 RQNSRSHRDNYFSTNSADIYGTMPKWNDDYQSRNRDWHSELDRHERGIERFGEEIEDLRIRSNKSERK 195
[Close]
BLAST of SMED30023112 vs. Planmine SMEST
Match: SMESG000038532.1 (SMESG000038532.1)

HSP 1 Score: 111.309 bits (277), Expect = 2.205e-30
Identity = 67/68 (98.53%), Postives = 67/68 (98.53%), Query Frame = -2 
Query:    1 RQNSRSHRDNYFSTNSADIYGTMPKWNDDYQSRNRDLHSELDRHXXXXXXXXXXXEDLRIRSNKSERK 204
            RQNSRSHRDNYFSTNSADIYGTMPKWNDDYQSRNRD HSELDRHERGIERFGEEIEDLRIRSNKSERK
Sbjct:  128 RQNSRSHRDNYFSTNSADIYGTMPKWNDDYQSRNRDWHSELDRHERGIERFGEEIEDLRIRSNKSERK 195
[Close]
BLAST of SMED30023112 vs. Planmine SMEST
Match: SMESG000038532.1 (SMESG000038532.1)

HSP 1 Score: 111.309 bits (277), Expect = 2.226e-30
Identity = 67/68 (98.53%), Postives = 67/68 (98.53%), Query Frame = -2 
Query:    1 RQNSRSHRDNYFSTNSADIYGTMPKWNDDYQSRNRDLHSELDRHXXXXXXXXXXXEDLRIRSNKSERK 204
            RQNSRSHRDNYFSTNSADIYGTMPKWNDDYQSRNRD HSELDRHERGIERFGEEIEDLRIRSNKSERK
Sbjct:  128 RQNSRSHRDNYFSTNSADIYGTMPKWNDDYQSRNRDWHSELDRHERGIERFGEEIEDLRIRSNKSERK 195
[Close]
BLAST of SMED30023112 vs. Planmine SMEST
Match: SMESG000038520.1 (SMESG000038520.1)

HSP 1 Score: 109.768 bits (273), Expect = 4.270e-30
Identity = 65/67 (97.01%), Postives = 65/67 (97.01%), Query Frame = -2 
Query:    1 QNSRSHRDNYFSTNSADIYGTMPKWNDDYQSRNRDLHSELDRHXXXXXXXXXXXEDLRIRSNKSERK 201
            QNSRSH DNYFSTNSADIYGTMPKWNDDYQSRNRDLHSELDRHERGIE FGEEIEDLRIRSNKSERK
Sbjct:  203 QNSRSHGDNYFSTNSADIYGTMPKWNDDYQSRNRDLHSELDRHERGIEIFGEEIEDLRIRSNKSERK 269
[Close]
BLAST of SMED30023112 vs. Planmine SMEST
Match: SMESG000047804.1 (SMESG000047804.1)

HSP 1 Score: 108.612 bits (270), Expect = 2.097e-29
Identity = 64/68 (94.12%), Postives = 65/68 (95.59%), Query Frame = -2 
Query:    1 RQNSRSHRDNYFSTNSADIYGTMPKWNDDYQSRNRDLHSELDRHXXXXXXXXXXXEDLRIRSNKSERK 204
            RQNSR H DNYFSTNSADIYGTMP+WNDDYQSRNRDLHSELDRHERGIE FGEEIEDLRIRSNKSERK
Sbjct:  202 RQNSRFHGDNYFSTNSADIYGTMPEWNDDYQSRNRDLHSELDRHERGIEIFGEEIEDLRIRSNKSERK 269
The following BLAST results are available for this feature:
BLAST of SMED30023112 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 SMED30023112 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 SMED30023112 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 SMED30023112 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 SMED30023112 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 SMED30023112 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 SMED30023112 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 SMED30023112 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 SMED30023112 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 SMED30023112 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 SMED30023112 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 SMED30023112 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 SMED30023112 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 SMED30023112 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000038532.12.184e-3098.53SMESG000038532.1[more]
SMESG000038532.12.205e-3098.53SMESG000038532.1[more]
SMESG000038532.12.226e-3098.53SMESG000038532.1[more]
SMESG000038520.14.270e-3097.01SMESG000038520.1[more]
SMESG000047804.12.097e-2994.12SMESG000047804.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023112 ID=SMED30023112|Name=SMED30023112|organism=Schmidtea mediterranea sexual|type=transcript|length=205bp
TTTTCTTTCTGATTTATTCGATCTTATTCTCAAATCCTCTATTTCTTCTC
CAAATCTTTCTATCCCCCTCTCGTGCCTATCTAATTCTGAATGCAAATCT
CTGTTCCGTGATTGATAATCATCATTCCACTTGGGCATTGTGCCATAAAT
ATCAGCCGAGTTGGTAGAAAAGTAATTGTCTCGATGGGATCTGCTGTTTT
GCCTC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 41..68