SMED30007604

Overview
NameSMED30007604
Smed IDSMED30007604
Length (bp)1793
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 SMED30007604 (SMED30007604) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007604 (SMED30007604) 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 SMED30007604 (SMED30007604) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007604 (SMED30007604) 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



SMED30007604

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
Smed sexual biotypeSMED30007604h1SMcG0000962 Contig49398uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007604h1SMcG0000962 Contig49398newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
protonephridiaSMED30007604h1SMcG0000962 dd_Smed_v4_4756_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30007604h1SMcG0000962 dd_Smed_v4_4756_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007604h1SMcG0000962 dd_Smed_v4_4756_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007604h1SMcG0000962 dd_Smed_v4_4756_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30007604h1SMcG0000962 dd_Smed_v4_3016_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30007604h1SMcG0000962 dd_Smed_v4_3016_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007604h1SMcG0000962 dd_Smed_v4_3016_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007604h1SMcG0000962 dd_Smed_v4_3016_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
dorsal ventral margin of the whole animalSMED30007604h1SMcG0000962 dd_Smed_v4_3016_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
SMED30007604 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007368:10606..20009 -8901
Homology
[Close]
BLAST of SMED30007604 vs. Planmine SMEST
Match: SMESG000074719.1 (SMESG000074719.1)

HSP 1 Score: 396.356 bits (1017), Expect = 2.563e-132
Identity = 218/219 (99.54%), Postives = 218/219 (99.54%), Query Frame = 2 
Query: 1049 PKSIEISNPITITNKPQIKKTTQKIFNSTPANKIDKSTKIATKLYKKYPEKSTSNGINSSKYKRVKTEKLVETTLRGKQKNSTPVSTNSRDWKTISKSHLQRPIQNYKKQNVSSENPANAYGGIKISTASHFLNSQYSIDNENMESTTTPNITMGAGXXXXXXXXXXXXXXXXXXXTALRRKMKKSRRSIVRVQSRDLDNTSERNQSQMIPLTKSEPND 1705
            PKSIEISNPITITNKPQIKKTTQKIFNSTPANKIDKSTKIATKLYKKYPEKSTSNGINSSKYKRVKTEKLVETTLRGKQKNSTPVSTNSR WKTISKSHLQRPIQNYKKQNVSSENPANAYGGIKISTASHFLNSQYSIDNENMESTTTPNITMGAGPLVIVVLLPFLALFLIAIVTALRRKMKKSRRSIVRVQSRDLDNTSERNQSQMIPLTKSEPND
Sbjct:  269 PKSIEISNPITITNKPQIKKTTQKIFNSTPANKIDKSTKIATKLYKKYPEKSTSNGINSSKYKRVKTEKLVETTLRGKQKNSTPVSTNSRHWKTISKSHLQRPIQNYKKQNVSSENPANAYGGIKISTASHFLNSQYSIDNENMESTTTPNITMGAGPLVIVVLLPFLALFLIAIVTALRRKMKKSRRSIVRVQSRDLDNTSERNQSQMIPLTKSEPND 487

HSP 2 Score: 322.783 bits (826), Expect = 1.038e-103
Identity = 187/188 (99.47%), Postives = 187/188 (99.47%), Query Frame = 2 
Query:  263 MKFSVNSTVSILSDPNSTLELLNGXXXXXXXXXXXXXXLSQITNLDKSFQTNATRTGLPKMSTTEIISLNETITKPVVLSQNLTSSKLKEPSSPGESSTKVFQKTTEKMKEKTFQTMKETQKQISESPTSIKLTSYRKSLSSENVKEKDNYSTISSSPSLTKQQNSNIIFSTKSFIIEETAEIKKISQ 826
            MKFSVNSTVSILSDPNSTLELLNGTNETVTVEVSNTSVLSQITNLDKSFQTNATRTGLPKMSTTEIISLNETITKPVVLSQNLTSSKLKEPSS GESSTKVFQKTTEKMKEKTFQTMKETQKQISESPTSIKLTSYRKSLSSENVKEKDNYSTISSSPSLTKQQNSNIIFSTKSFIIEETAEIKKISQ
Sbjct:    1 MKFSVNSTVSILSDPNSTLELLNGTNETVTVEVSNTSVLSQITNLDKSFQTNATRTGLPKMSTTEIISLNETITKPVVLSQNLTSSKLKEPSSTGESSTKVFQKTTEKMKEKTFQTMKETQKQISESPTSIKLTSYRKSLSSENVKEKDNYSTISSSPSLTKQQNSNIIFSTKSFIIEETAEIKKISQ 188
The following BLAST results are available for this feature:
BLAST of SMED30007604 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 SMED30007604 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 SMED30007604 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 SMED30007604 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 SMED30007604 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 SMED30007604 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 SMED30007604 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 SMED30007604 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 SMED30007604 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 SMED30007604 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 SMED30007604 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 SMED30007604 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 SMED30007604 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 SMED30007604 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000074719.12.563e-13299.54SMESG000074719.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007604 ID=SMED30007604|Name=SMED30007604|organism=Schmidtea mediterranea sexual|type=transcript|length=1793bp
ACATTTTTGCACAAATCAACGACCAAATTCGAATTAATAATTGGTGTAGT
CTGAGTCTGATTAAAACAACAATTGAAATAACAATACGTTTGATAGCACA
CAGCACCTATCAACAACATTAAATCAAGAAGTGCTATGATAACCTGAATC
TGAAATATGGAGATGTGCAAATTAAATCTACATAATAGGAGAGGGTCTAT
GATGTGCTAATTTGCATTTGCATTTTCGATTTACTTGAACGTTTTTCTCA
TTACTGATAACAATGAAATTCAGTGTAAATTCAACAGTGAGTATTTTATC
AGATCCGAATTCAACTTTGGAATTGTTAAATGGTACAAACGAAACGGTCA
CAGTTGAAGTTTCAAATACGTCTGTTTTATCACAAATCACAAATTTGGAC
AAGTCTTTTCAAACGAATGCAACTAGAACTGGTCTACCAAAAATGTCAAC
AACAGAAATCATTAGTTTGAATGAAACTATCACGAAGCCAGTGGTGTTAT
CTCAAAATTTAACGTCGTCCAAGTTGAAGGAACCCAGTTCCCCAGGTGAA
TCCTCAACGAAGGTTTTCCAGAAAACAACCGAGAAAATGAAAGAAAAGAC
TTTTCAAACTATGAAAGAAACACAGAAACAAATTTCGGAATCTCCAACTA
GTATAAAATTAACTTCATATAGAAAATCATTGAGTTCGGAAAATGTAAAA
GAAAAAGATAATTACTCAACAATTTCTTCTTCACCGAGTTTGACAAAACA
ACAAAACTCCAATATTATATTTTCAACAAAATCTTTTATTATCGAAGAAA
CAGCAGAAATTAAAAAAATATCTCAGACCAGTCCTCAAACAACAACAATA
ACAACACCAAGAACTACCACCATCACAACAACAACAATGACAACAAAACC
AACAACAACAACAGCAACAACAACAACAACAACAAAAACACCAACTGAAA
CACTGCCACCTTCATTACCGTCAACAAAAAATACAATAACAAGTACTGAA
AATATAATCAAGGAGAAAAAAACAAAAGAAAATTTTGAAAATACTACACC
GAAATCAATTGAAATCTCCAATCCAATTACAATAACAAATAAACCACAAA
TCAAAAAAACAACTCAAAAAATATTTAACAGTACTCCTGCAAATAAAATC
GACAAATCTACAAAAATAGCCACAAAACTTTACAAAAAATATCCAGAAAA
GTCCACCTCGAATGGTATCAACTCGAGCAAATATAAAAGAGTTAAAACCG
AAAAATTGGTTGAAACGACTCTCAGAGGAAAACAGAAAAATTCCACTCCA
GTTTCCACGAACAGTCGCGATTGGAAAACTATCTCAAAATCACACCTTCA
AAGACCCATACAAAACTATAAAAAACAGAATGTTTCATCTGAAAATCCTG
CCAATGCCTATGGAGGGATTAAAATTTCCACGGCGTCTCATTTCCTAAAT
TCTCAATACTCTATTGACAATGAAAATATGGAGTCTACGACTACACCGAA
CATTACAATGGGAGCTGGTCCTCTTGTTATTGTTGTTCTCTTGCCATTTC
TTGCGCTTTTTTTAATTGCTATAGTCACTGCTTTACGAAGAAAAATGAAA
AAGTCCCGTAGAAGCATTGTTCGAGTTCAGAGCAGAGATCTCGATAACAC
ATCGGAAAGAAATCAAAGCCAAATGATACCCCTGACCAAGTCGGAACCGA
ATGATTGAAGGGAATGAAATTAGTGCCATAGGCAAATAGTTAATTTTGAA
TTTAAATTTTAGATTGGTGTTTGAAATTATCTGACTTGTTTGT
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protein sequence of SMED30007604-orf-1

>SMED30007604-orf-1 ID=SMED30007604-orf-1|Name=SMED30007604-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=482bp
MKFSVNSTVSILSDPNSTLELLNGTNETVTVEVSNTSVLSQITNLDKSFQ
TNATRTGLPKMSTTEIISLNETITKPVVLSQNLTSSKLKEPSSPGESSTK
VFQKTTEKMKEKTFQTMKETQKQISESPTSIKLTSYRKSLSSENVKEKDN
YSTISSSPSLTKQQNSNIIFSTKSFIIEETAEIKKISQTSPQTTTITTPR
TTTITTTTMTTKPTTTTATTTTTTKTPTETLPPSLPSTKNTITSTENIIK
EKKTKENFENTTPKSIEISNPITITNKPQIKKTTQKIFNSTPANKIDKST
KIATKLYKKYPEKSTSNGINSSKYKRVKTEKLVETTLRGKQKNSTPVSTN
SRDWKTISKSHLQRPIQNYKKQNVSSENPANAYGGIKISTASHFLNSQYS
IDNENMESTTTPNITMGAGPLVIVVLLPFLALFLIAIVTALRRKMKKSRR
SIVRVQSRDLDNTSERNQSQMIPLTKSEPND*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000026gut
PLANA:0000043dorsal ventral margin of the whole animal
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 468..487
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 84..102
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 465..487
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 84..107
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 135..162
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 212..239
NoneNo IPR availableTMHMMTMhelixcoord: 425..447