SMED30018756

Overview
NameSMED30018756
Smed IDSMED30018756
Length (bp)941
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30018756 (SMED30018756) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018756 (SMED30018756) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30018756

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



PAGE Curations: 24

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pigment cellSMED30018756h1SMcG0009448 SmedASXL_018069SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017
whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0009453 Contig51576newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0003718 Contig53462uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0003718 Contig53462newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0003719 Contig53462uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0003719 Contig53462newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0009392 Contig53462uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0009392 Contig53462newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0009453 Contig53462uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0009453 Contig53462newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0009448 Contig53462uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0009448 Contig53462newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0009389 Contig53462uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018756h1SMcG0009389 Contig53462newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
gutSMED30018756h1SMcG0009448 dd_Smed_v4_12511_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30018756h1SMcG0009448 dd_Smed_v4_6916_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30018756h1SMcG0009448 Contig31713newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30018756h1SMcG0009448 Contig268newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30018756h1SMcG0009448 Contig268uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30018756h1SMcG0009448 Contig44991uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30018756h1SMcG0009448 Contig44991newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30018756 Contig27481newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30018756 Contig44038newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30018756 Contig44038uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30018756 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001681:19616..26507 -2096
Homology
BLAST of SMED30018756 vs. Planmine SMEST
Match: SMESG000079565.1 (SMESG000079565.1)

HSP 1 Score: 114.39 bits (285), Expect = 7.260e-31
Identity = 53/62 (85.48%), Postives = 57/62 (91.94%), Query Frame = -3
Query:  697 KLATTCGGDIDPVNKTIRSFISAELFYDLQGLISRNESRLEMSLTILNPDPNACSDPAETLP 882
            +LATTCGG IDPVNKT +SFISAELFYDLQGLISRNESRL+MSLTI NPDPNAC+DPA T P
Sbjct:  100 RLATTCGGHIDPVNKTNKSFISAELFYDLQGLISRNESRLQMSLTIHNPDPNACADPALTAP 161          
BLAST of SMED30018756 vs. Planmine SMEST
Match: SMESG000079563.1 (SMESG000079563.1)

HSP 1 Score: 110.923 bits (276), Expect = 2.471e-30
Identity = 55/80 (68.75%), Postives = 63/80 (78.75%), Query Frame = -3
Query:  520 MSLTILNPDPNACSDPAETLPKNAAVIRDNNIHSAGTSARSWNEASMRIGFIAGIVSICIALMVGIIAMCLSPRCAGLAD 759
            MSLTILNPDPNAC+DPAET PKN AVI+DNNIHSAGTSA  WN  S  I  IAG++ ICIAL VGIIA+ LS +   ++D
Sbjct:    1 MSLTILNPDPNACADPAETFPKNVAVIKDNNIHSAGTSAPIWNGTSRLIWIIAGMIFICIALAVGIIAIYLSLKLEKISD 80          
BLAST of SMED30018756 vs. Planmine SMEST
Match: SMESG000079563.1 (SMESG000079563.1)

HSP 1 Score: 110.153 bits (274), Expect = 4.745e-30
Identity = 55/80 (68.75%), Postives = 63/80 (78.75%), Query Frame = -3
Query:  520 MSLTILNPDPNACSDPAETLPKNAAVIRDNNIHSAGTSARSWNEASMRIGFIAGIVSICIALMVGIIAMCLSPRCAGLAD 759
            MSLTILNPDPNAC+DPAET PKN AVI+DNNIHSAGTSA  WN  S  I  IAG++ ICIAL VGIIA+ LS +   ++D
Sbjct:    1 MSLTILNPDPNACADPAETFPKNVAVIKDNNIHSAGTSAPIWNGTSRLIWIIAGMIFICIALAVGIIAIYLSLKLEKISD 80          
BLAST of SMED30018756 vs. Planmine SMEST
Match: SMESG000079579.1 (SMESG000079579.1)

HSP 1 Score: 116.316 bits (290), Expect = 5.504e-30
Identity = 61/97 (62.89%), Postives = 72/97 (74.23%), Query Frame = -3
Query:  607 KLATTCGGDIDPVNKTIRSFISAELFYDLQGLISRNESRLEMSLTILNPDPNACSDP-----AETLPKNAAVIRDNNIHSAGTSARSWNEASMRIGF 882
            +LATTCGG IDPVN+TI+SFISAELFYDLQGLISRNESRLEMSLTILNPDPNAC+DP     A  L  + +++   N  SAGT     + +   IG+
Sbjct:   97 RLATTCGGHIDPVNQTIKSFISAELFYDLQGLISRNESRLEMSLTILNPDPNACADPDQRTSATILKLDKSIVA--NQESAGTGKDKPDASDWSIGY 191          
BLAST of SMED30018756 vs. Planmine SMEST
Match: SMESG000079563.1 (SMESG000079563.1)

HSP 1 Score: 112.849 bits (281), Expect = 3.575e-29
Identity = 55/80 (68.75%), Postives = 63/80 (78.75%), Query Frame = -3
Query:  520 MSLTILNPDPNACSDPAETLPKNAAVIRDNNIHSAGTSARSWNEASMRIGFIAGIVSICIALMVGIIAMCLSPRCAGLAD 759
            MSLTILNPDPNAC+DPAET PKN AVI+DNNIHSAGTSA  WN  S  I  IAG++ ICIAL VGIIA+ LS +   ++D
Sbjct:    1 MSLTILNPDPNACADPAETFPKNVAVIKDNNIHSAGTSAPIWNGTSRLIWIIAGMIFICIALAVGIIAIYLSLKLEKISD 80          
The following BLAST results are available for this feature:
BLAST of SMED30018756 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 SMED30018756 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 SMED30018756 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 SMED30018756 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 SMED30018756 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 SMED30018756 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 SMED30018756 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 SMED30018756 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 SMED30018756 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 SMED30018756 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 SMED30018756 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 SMED30018756 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 SMED30018756 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 SMED30018756 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000079565.17.260e-3185.48SMESG000079565.1[more]
SMESG000079563.12.471e-3068.75SMESG000079563.1[more]
SMESG000079563.14.745e-3068.75SMESG000079563.1[more]
SMESG000079579.15.504e-3062.89SMESG000079579.1[more]
SMESG000079563.13.575e-2968.75SMESG000079563.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018756 ID=SMED30018756|Name=SMED30018756|organism=Schmidtea mediterranea sexual|type=transcript|length=941bp
TATGGAGTAGAAGAAAAAAATTCCTATGGGCATATTTATTTGAAAATTGT
CAAAAATAGCATGTAAAACAAATTTATTTTAACTTTATTTTGGTCAAAAA
CCCAGCTGATATTGACCATCGTTTGAATCTATCCTAATGTAACACGTTGA
ATAAAAGAGAGGAAGCTCTTAGATATCAATCAAAGGGATTTAGATTTAAA
GATCCGTGCAGCCAATATGTTTGATGTTTTAGGACAATCGTACGTTGGTT
AGACGCTAAAGACCTATTCTACTATTATATGCTGGTAGGTAATAAGAGGA
TAATCATCATGTCATATATAACATTGACGTTGAAGCTACATTGAAATATT
GCAAATTTTTTGTAAATGGGGTAAAACGATTTTAATATTATGTTATAAAC
TAGAAATAAAAGAATTAATGCACAATAAAAGGTGGCCATTACTCTCAGCT
GATGAAATTGGAACATTCATCTAGATCTTGAGAGATTTTTACTGAGCTCC
TTAGTGACCTCCAAATCTTATCCGCGAGTCCCGCACATCTAGGAGATAAA
CACATCGCAATAATTCCAACCATCAAAGCAATGCATATAGATACGATGCC
AGCAATGAACCCGATCCTCATGGAAGCCTCATTCCAACTCCTTGCAGATG
TGCCAGCTGAATGGATATTATTATCCCTGATCACAGCGGCATTCTTTGGT
AATGTTTCAGCCGGATCTGAACAAGCATTTGGATCTGGATTAAGAATTGT
CAAACTCATTTCCAATCGGGATTCATTTCTACTAATCAAGCCTTGCAGAT
CATAAAACAGTTCAGCACTAATAAATGATCTAATTGTCTTATTGACCGGG
TCAATGTCACCGCCACAAGTTGTAGCAAGCTTAGTAAAGGGAAATCTCAA
TTACATCTCGCATTCCAATTAGATAATACTCGATATGTCCG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0002089reproductive organ