SMED30001870

Overview
NameSMED30001870
Smed IDSMED30001870
Length (bp)1471
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



SMED30001870

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30001870 SmedASXL_016348SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
protonephridiaSMED30001870 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30001870 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30001870 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001870 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30001870 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
cilated neuronSMED30001870 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30001870 dd_Smed_v6_4311_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30001870 Contig43299newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30001870 Contig43299uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30001870 dd_Smed_v4_4311_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30001870 dd_Smed_v4_4311_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
The following BLAST results are available for this feature:
BLAST of SMED30001870 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 SMED30001870 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 SMED30001870 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 SMED30001870 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 SMED30001870 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 SMED30001870 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 SMED30001870 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 SMED30001870 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 SMED30001870 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 SMED30001870 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 SMED30001870 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 SMED30001870 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 SMED30001870 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 SMED30001870 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001870 ID=SMED30001870|Name=SMED30001870|organism=Schmidtea mediterranea sexual|type=transcript|length=1471bp
CACTACTACAGATATAACTCCATCAATCCATTAACAGTTCTCCTTTACAT
ATTTTATCTGGTCAATCTACAAACAGTTTCATAACATCAAGTCAATCAGC
TTTCTCAGACAGTTCATCATTCTCCAACTCTAAATTTCAGTCTGCTCCCA
TATATTCAACAGATACTCCGTTTTCACCTAATCCATCCGCAATGACCAAT
TCACTGTTTCCTTCAAATATACCAATTCAATCTACTCCAATTCCTTCAAT
AAGCTATACTCCACAATCTAGTAACGTACCATTTTTAACAAATTCCTCAA
ACACTTCATCAACATCATCTTCTCCTACGTCTGTCTCTGTGACTAACCTT
CCAAGTAATTCATCAACATCGGGAGCATCAGCAGATATGGTACTATCAAC
AATTTCTAGTGCAATGTTAGCATCAGTAACTTCACCTATGTCTTTGGTCA
GCTACCTGCCAATTCAACCCGGAGAATTCGAANNNNNNNNNNNNNNNNNA
TGTGAAATTCCTCAACGATATCTTCACCGCTGCCGTCAGCAATTCGAGTT
CCGTTGTGTACAAATCCTATATTCAAAATATGACGTCCGTTATCAATCAA
GGGATCAGAAATTATGGGATGAGGACGCTGAATATTTTAGTTAATTCCAT
TAGTCCTGGAAGTGTTGTCGTAGACTTCAATTGGAATCTTGCTTCGAATA
TTTCAACTAGTTATTCAACCATAAGAAATACAATATCAAATANNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACA
AGGACCAACAATCCCGTCAAACATAATAACATCAGAAGTCCCATCAACAT
TTTTGAATACGAATGCTATTTCACCAACATCATCCGTGGGAAATATTCAG
TCTCAATCAACTTCTTTCTTAAATATAAGTTCAGTTATAACGCAATCGTC
TTTATCAGTTACTGCGCCTGTAACATCAGCCGCGCCAGTGTTCAACAGTT
CTCTTTCTATTATTTCTACTGACCCTGTGACAACAAATATAAGTTCGACA
AATGCGGTGTCTACATCTTTAACTAATACAATTACAACTACACCAGTGTT
GAACAATTCTTTTTCAACGGAAAGTTCAAGTCCTCTCTCTACAACATTAT
CAAATTTCTACTCGACCACTTCAATTCCCTTGTCTGTTGAAAATACAACG
ACCATAACTCCAATGGTAAATATGTCAGTTTCAACAGCAAGTTTCAATTC
TGTCTCTGATACAATATCAAATGCGTATTTATTAAACGCATCAACTACGG
CCACCGTTTCATTAACAAATAATTCCATTCCACCTTTTTCTTCAACGATT
CCCTCAAATATAAATCAACCAACAACAACGAGCAGTATGACAAACGCCAC
GACGTCAACTCCAGTTGCCAACTCTTCGTTATCAACGCCACAAATAACCT
CCTCGACTTCAGTATCAACTA
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protein sequence of SMED30001870-orf-1

>SMED30001870-orf-1 ID=SMED30001870-orf-1|Name=SMED30001870-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=151bp
MTNSLFPSNIPIQSTPIPSISYTPQSSNVPFLTNSSNTSSTSSSPTSVSV
TNLPSNSSTSGASADMVLSTISSAMLASVTSPMSLVSYLPIQPGEFEXXX
XXXCEIPQRYLHRCRQQFEFRCVQILYSKYDVRYQSRDQKLWDEDAEYFS
*
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protein sequence of SMED30001870-orf-2

>SMED30001870-orf-2 ID=SMED30001870-orf-2|Name=SMED30001870-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=297bp
MTSVINQGIRNYGMRTLNILVNSISPGSVVVDFNWNLASNISTSYSTIRN
TISNXXXXXXXXXXXXXXXXXXXQGPTIPSNIITSEVPSTFLNTNAISPT
SSVGNIQSQSTSFLNISSVITQSSLSVTAPVTSAAPVFNSSLSIISTDPV
TTNISSTNAVSTSLTNTITTTPVLNNSFSTESSSPLSTTLSNFYSTTSIP
LSVENTTTITPMVNMSVSTASFNSVSDTISNAYLLNASTTATVSLTNNSI
PPFSSTIPSNINQPTTTSSMTNATTSTPVANSSLSTPQITSSTSVST
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000096ventral epidermis
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002032epidermal cell