SMED30010867

Overview
NameSMED30010867
Smed IDSMED30010867
Length (bp)451
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



SMED30010867

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



PAGE Curations: 16

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30010867h1SMcG0009621 Contig6838newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30010867h1SMcG0009621 Contig6838uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Smed sexual biotypeSMED30010867h1SMcG0009621 Contig53740uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010867h1SMcG0009621 Contig53740newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010867h1SMcG0009621 Contig6838newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010867h1SMcG0009621 Contig6838uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30010867h1SMcG0009621 dd_Smed_v4_2345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30010867h1SMcG0009621 dd_Smed_v4_2345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30010867h1SMcG0009621 dd_Smed_v4_2345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30010867h1SMcG0009621 dd_Smed_v4_2345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30010867h1SMcG0009621 dd_Smed_v4_2345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30010867h1SMcG0009621 dd_Smed_v4_2345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30010867h1SMcG0009621 dd_Smed_v4_2345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30010867h1SMcG0009621 dd_Smed_v4_2345_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30010867h1SMcG0009621 dd_Smed_v6_2345_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30010867h1SMcG0009621 dd_Smed_v4_2345_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
Homology
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BLAST of SMED30010867 vs. Planmine SMEST
Match: SMESG000007021.1 (SMESG000007021.1)

HSP 1 Score: 73.9442 bits (180), Expect = 1.724e-29
Identity = 49/98 (50.00%), Postives = 55/98 (56.12%), Query Frame = -2 
Query:  181 DGRAFRKLL-----NLQLLFNNECFQQID---VDYILAQKMALIISASLEEKIASFQF*KPIAYKRYVDKRT*NGF*IL*SLHNNTVFTCEIEIKSHL 450
            D RAFRKLL     N+  LFN+E +QQID   +   LA  MA I  ASLE+KIASFQF KP  YK               SLH N VFTCE E KS +
Sbjct:   65 DRRAFRKLLEFATSNVNFLFNDEWYQQIDGVAMGSPLAPTMASIFLASLEKKIASFQFEKPFVYK---------------SLHKNIVFTCETERKSSI 147

HSP 2 Score: 53.1434 bits (126), Expect = 1.724e-29
Identity = 24/44 (54.55%), Postives = 32/44 (72.73%), Query Frame = -1 
Query:   65 DKKSSIVFTDL*FQ*NDKHYKTEVYGKPSDTGLYTFPDNSVNYK 196
            ++KSSI F DL  Q  DK Y+TE+Y KP+DTGLYT P++   +K
Sbjct:  142 ERKSSIAFLDLLIQRKDKQYETEIYRKPTDTGLYTSPESFCEFK 185

HSP 3 Score: 38.891 bits (89), Expect = 1.724e-29
Identity = 19/25 (76.00%), Postives = 20/25 (80.00%), Query Frame = -3 
Query:    6 FCEL*DKYKRIMTKGLIYRSWSLSS 80
            FCE   KYKR M KGLIYRSW+LSS
Sbjct:  181 FCEF--KYKRNMVKGLIYRSWALSS 203
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BLAST of SMED30010867 vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 83.9593 bits (206), Expect = 2.201e-23
Identity = 55/112 (49.11%), Postives = 64/112 (57.14%), Query Frame = -2 
Query:  166 DGRAFRKLL-----NLQLLFNNECFQQID---VDYILAQKMALIISASLEEKIASFQF*KPIAYKRYVD---------KRT*NGF*IL*SLHNNTVFTCEIEIKSHLLCLRI 450
            DGRAFRKL+     N+  LFN+E +QQID   +   LA  MA I  ASLE+KIASFQF KP  YKRYVD         K        + SLH N VFTCE E KS +  L +
Sbjct: 1597 DGRAFRKLIEFATSNVNFLFNDEWYQQIDGVAMGSPLAPTMASIFLASLEKKIASFQFEKPFVYKRYVDDIFLEFENQKHVEPFLHFMNSLHKNLVFTCETERKSSIAFLDL 1708

HSP 2 Score: 41.5874 bits (96), Expect = 2.201e-23
Identity = 19/25 (76.00%), Postives = 20/25 (80.00%), Query Frame = -3 
Query:    6 FCEL*DKYKRIMTKGLIYRSWSLSS 80
            FCE   +YKR M KGLIYRSWSLSS
Sbjct: 1737 FCEF--RYKRNMVKGLIYRSWSLSS 1759

HSP 3 Score: 60.4622 bits (145), Expect = 3.107e-11
Identity = 30/61 (49.18%), Postives = 41/61 (67.21%), Query Frame = -1 
Query:   80 HVEWFLNFMKFT*QHCIHM*NRDKKSSIVFTDL*FQ*NDKHYKTEVYGKPSDTGLYTFPDN 262
            HVE FL+FM    ++ +     ++KSSI F DL  Q  DK Y+TE+Y KP+DTGLYT P++
Sbjct: 1676 HVEPFLHFMNSLHKNLVFTCETERKSSIAFLDLLIQRKDKQYETEIYRKPTDTGLYTSPES 1736
[Close]
BLAST of SMED30010867 vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 83.9593 bits (206), Expect = 2.495e-23
Identity = 55/112 (49.11%), Postives = 64/112 (57.14%), Query Frame = -2 
Query:  166 DGRAFRKLL-----NLQLLFNNECFQQID---VDYILAQKMALIISASLEEKIASFQF*KPIAYKRYVD---------KRT*NGF*IL*SLHNNTVFTCEIEIKSHLLCLRI 450
            DGRAFRKL+     N+  LFN+E +QQID   +   LA  MA I  ASLE+KIASFQF KP  YKRYVD         K        + SLH N VFTCE E KS +  L +
Sbjct: 2554 DGRAFRKLIEFATSNVNFLFNDEWYQQIDGVAMGSPLAPTMASIFLASLEKKIASFQFEKPFVYKRYVDDIFLEFENQKHVEPFLHFMNSLHKNLVFTCETERKSSIAFLDL 2665

HSP 2 Score: 41.5874 bits (96), Expect = 2.495e-23
Identity = 19/25 (76.00%), Postives = 20/25 (80.00%), Query Frame = -3 
Query:    6 FCEL*DKYKRIMTKGLIYRSWSLSS 80
            FCE   +YKR M KGLIYRSWSLSS
Sbjct: 2694 FCEF--RYKRNMVKGLIYRSWSLSS 2716

HSP 3 Score: 60.4622 bits (145), Expect = 3.309e-11
Identity = 30/61 (49.18%), Postives = 41/61 (67.21%), Query Frame = -1 
Query:   80 HVEWFLNFMKFT*QHCIHM*NRDKKSSIVFTDL*FQ*NDKHYKTEVYGKPSDTGLYTFPDN 262
            HVE FL+FM    ++ +     ++KSSI F DL  Q  DK Y+TE+Y KP+DTGLYT P++
Sbjct: 2633 HVEPFLHFMNSLHKNLVFTCETERKSSIAFLDLLIQRKDKQYETEIYRKPTDTGLYTSPES 2693
[Close]
BLAST of SMED30010867 vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 83.9593 bits (206), Expect = 2.724e-23
Identity = 55/112 (49.11%), Postives = 64/112 (57.14%), Query Frame = -2 
Query:  166 DGRAFRKLL-----NLQLLFNNECFQQID---VDYILAQKMALIISASLEEKIASFQF*KPIAYKRYVD---------KRT*NGF*IL*SLHNNTVFTCEIEIKSHLLCLRI 450
            DGRAFRKL+     N+  LFN+E +QQID   +   LA  MA I  ASLE+KIASFQF KP  YKRYVD         K        + SLH N VFTCE E KS +  L +
Sbjct: 1663 DGRAFRKLIEFATSNVNFLFNDEWYQQIDGVAMGSPLAPTMASIFLASLEKKIASFQFEKPFVYKRYVDDIFLEFENQKHVEPFLHFMNSLHKNLVFTCETERKSSIAFLDL 1774

HSP 2 Score: 41.2022 bits (95), Expect = 2.724e-23
Identity = 19/25 (76.00%), Postives = 20/25 (80.00%), Query Frame = -3 
Query:    6 FCEL*DKYKRIMTKGLIYRSWSLSS 80
            FCE   +YKR M KGLIYRSWSLSS
Sbjct: 1803 FCEF--RYKRNMVKGLIYRSWSLSS 1825

HSP 3 Score: 60.4622 bits (145), Expect = 3.142e-11
Identity = 30/61 (49.18%), Postives = 41/61 (67.21%), Query Frame = -1 
Query:   80 HVEWFLNFMKFT*QHCIHM*NRDKKSSIVFTDL*FQ*NDKHYKTEVYGKPSDTGLYTFPDN 262
            HVE FL+FM    ++ +     ++KSSI F DL  Q  DK Y+TE+Y KP+DTGLYT P++
Sbjct: 1742 HVEPFLHFMNSLHKNLVFTCETERKSSIAFLDLLIQRKDKQYETEIYRKPTDTGLYTSPES 1802
[Close]
BLAST of SMED30010867 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 71.2478 bits (173), Expect = 6.139e-23
Identity = 47/98 (47.96%), Postives = 59/98 (60.20%), Query Frame = -2 
Query:  181 DGRAFRKLL-----NLQLLFNNECFQQID---VDYILAQKMALIISASLEEKIASFQF*KPIAYKRYVDKRT*NGF*IL*SLHNNTVFTCEIEIKSHL 450
            D RAFRK+L     N+  LFN+E +QQID   +   LA  MA I  ASLE+KIASFQF KP+    ++ +     F  + SLH N VFTCE E KS +
Sbjct:  132 DRRAFRKILEFATSNVNFLFNDEWYQQIDGVAMGSPLAPTMASIFLASLEKKIASFQFEKPL----FIKETCRTVFAFMNSLHKNIVFTCETERKSSI 225

HSP 2 Score: 52.7582 bits (125), Expect = 6.139e-23
Identity = 23/45 (51.11%), Postives = 32/45 (71.11%), Query Frame = -1 
Query:   62 DKKSSIVFTDL*FQ*NDKHYKTEVYGKPSDTGLYTFPDNSVNYKI 196
            ++KSSI F DL  Q  DK Y+TE+Y KP+DTGLYT P++   + +
Sbjct:  220 ERKSSIAFLDLLIQRKDKQYETEIYRKPTDTGLYTSPESVCEFNV 264
The following BLAST results are available for this feature:
BLAST of SMED30010867 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 SMED30010867 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 SMED30010867 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 SMED30010867 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 SMED30010867 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 SMED30010867 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 SMED30010867 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 SMED30010867 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 SMED30010867 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 SMED30010867 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 SMED30010867 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 SMED30010867 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 SMED30010867 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 SMED30010867 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000007021.11.724e-2950.00SMESG000007021.1[more]
SMESG000050479.12.201e-2349.11SMESG000050479.1[more]
SMESG000050479.12.495e-2349.11SMESG000050479.1[more]
SMESG000050479.12.724e-2349.11SMESG000050479.1[more]
SMESG000044971.16.139e-2347.96SMESG000044971.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010867 ID=SMED30010867|Name=SMED30010867|organism=Schmidtea mediterranea sexual|type=transcript|length=451bp
AAAATAGAAGATAAAGACCATGAACGATAAATCAGTCCTTTCGTCATAAT
TCTCTTATACTTATCTTATAATTCACAGAATTGTCAGGAAAAGTATAAAG
ACCAGTATCACTTGGTTTGCCATAAACCTCTGTCTTATAGTGTTTATCGT
TTCATTGGAATTATAAATCCGTAAACACAATAGATGACTTTTTATCTCTA
TTTCACATGTGAATACAGTGTTGTTATGTAAACTTCATAAAATTCAAAAA
CCATTCTACGTGCGTTTATCTACATACCGTTTATAAGCAATGGGTTTCTA
AAATTGGAAAGAAGCAATTTTCTCTTCTAAGCTTGCCGAAATTATTAATG
CCATCTTTTGTGCTAAAATATAATCCACATCTATTTGTTGAAAACATTCA
TTATTGAAAAGAAGTTGCAAATTCAAAAGTTTACGAAATGCCCTTCCATC
C
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