SMED30004024

Overview
NameSMED30004024
Smed IDSMED30004024
Length (bp)1649
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 SMED30004024 (SMED30004024) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004024 (SMED30004024) 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 SMED30004024 (SMED30004024) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004024 (SMED30004024) 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




SMED30004024

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30004024h1SMcG0022156 Contig54582newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30004024h1SMcG0022156 dd_Smed_v4_2123_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30004024h1SMcG0022156 dd_Smed_v4_2123_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30004024h1SMcG0022156 dd_Smed_v4_2123_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
glial cellSMED30004024h1SMcG0022156 dd_Smed_v6_2123_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30004024 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002110:2241..9693 +8058
Homology
BLAST of SMED30004024 vs. Planmine SMEST
Match: SMESG000022827.1 (SMESG000022827.1)

HSP 1 Score: 317.39 bits (812), Expect = 3.659e-106
Identity = 153/154 (99.35%), Postives = 153/154 (99.35%), Query Frame = 1
Query:    4 RLKIYANISKLSIYLMNDYDFFSKISLQSAFICPVYNTAMQNLGYQRQRSTWTLYSKPSNDTIIENIFKYCFYSYIVKRKEQPYSEPRNKNFTKSFDSGDYRNKDRNTHSPYRNRQNFPQEDRNRPPFRKPNQCNYQKKSSFGEENHQQRSVGL 465
            RL IYANISKLSIYLMNDYDFFSKISLQSAFICPVYNTAMQNLGYQRQRSTWTLYSKPSNDTIIENIFKYCFYSYIVKRKEQPYSEPRNKNFTKSFDSGDYRNKDRNTHSPYRNRQNFPQEDRNRPPFRKPNQCNYQKKSSFGEENHQQRSVGL
Sbjct:   59 RLDIYANISKLSIYLMNDYDFFSKISLQSAFICPVYNTAMQNLGYQRQRSTWTLYSKPSNDTIIENIFKYCFYSYIVKRKEQPYSEPRNKNFTKSFDSGDYRNKDRNTHSPYRNRQNFPQEDRNRPPFRKPNQCNYQKKSSFGEENHQQRSVGL 212          
BLAST of SMED30004024 vs. Planmine SMEST
Match: SMESG000022827.1 (SMESG000022827.1)

HSP 1 Score: 309.301 bits (791), Expect = 2.472e-101
Identity = 150/151 (99.34%), Postives = 150/151 (99.34%), Query Frame = 1
Query:    4 RLKIYANISKLSIYLMNDYDFFSKISLQSAFICPVYNTAMQNLGYQRQRSTWTLYSKPSNDTIIENIFKYCFYSYIVKRKEQPYSEPRNKNFTKSFDSGDYRNKDRNTHSPYRNRQNFPQEDRNRPPFRKPNQCNYQKKSSFGEENHQQRS 456
            RL IYANISKLSIYLMNDYDFFSKISLQSAFICPVYNTAMQNLGYQRQRSTWTLYSKPSNDTIIENIFKYCFYSYIVKRKEQPYSEPRNKNFTKSFDSGDYRNKDRNTHSPYRNRQNFPQEDRNRPPFRKPNQCNYQKKSSFGEENHQQRS
Sbjct:   59 RLDIYANISKLSIYLMNDYDFFSKISLQSAFICPVYNTAMQNLGYQRQRSTWTLYSKPSNDTIIENIFKYCFYSYIVKRKEQPYSEPRNKNFTKSFDSGDYRNKDRNTHSPYRNRQNFPQEDRNRPPFRKPNQCNYQKKSSFGEENHQQRS 209          
BLAST of SMED30004024 vs. Planmine SMEST
Match: SMESG000022832.1 (SMESG000022832.1)

HSP 1 Score: 137.502 bits (345), Expect = 3.799e-34
Identity = 65/89 (73.03%), Postives = 73/89 (82.02%), Query Frame = 1
Query:    1 TRLKIYANISKLSIYLMNDYDFFSKISLQSAFICPVYNTAMQNLGYQRQRSTWTLYSKPSNDTIIENIFKYCFYSYIVKRKEQPYSEPR 267
            TRLKIYANISKLSIYLMND++FF+  SLQSAFIC  Y T M+NLGYQ+Q STW L +KPSND IIENIFKYCFYSYIVK K +   E +
Sbjct:   59 TRLKIYANISKLSIYLMNDFEFFTAASLQSAFICLTYETEMENLGYQKQNSTWILRNKPSNDQIIENIFKYCFYSYIVKDKRKEKDEDK 147          
BLAST of SMED30004024 vs. Planmine SMEST
Match: SMESG000022825.1 (SMESG000022825.1)

HSP 1 Score: 47.7506 bits (112), Expect = 3.113e-6
Identity = 22/88 (25.00%), Postives = 50/88 (56.82%), Query Frame = 1
Query:    4 RLKIYANISKLSIYLMNDYDFFSKISLQSAFICPVYNTAMQNLGYQRQRSTWTLYS--KPSNDTIIENIFKYCFYSYIVKRKEQPYSE 261
             ++I+  IS+L++ L  +++FF  +  ++     +Y+  +QNLGY+   + W   +  KP    ++EN+F +CF +++ + +    S+
Sbjct:   56 HIQIWKEISRLTVDLFLEFEFFRTLIFENQTPDEIYHERLQNLGYKLIDNNWQYINNQKPDIKVVVENVFIFCFLNHLYRVRHDSLSQ 143          
The following BLAST results are available for this feature:
BLAST of SMED30004024 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 SMED30004024 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 SMED30004024 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 SMED30004024 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 SMED30004024 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 SMED30004024 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 SMED30004024 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 SMED30004024 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 SMED30004024 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 SMED30004024 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 SMED30004024 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 SMED30004024 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 SMED30004024 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 SMED30004024 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000022827.13.659e-10699.35SMESG000022827.1[more]
SMESG000022827.12.472e-10199.34SMESG000022827.1[more]
SMESG000022832.13.799e-3473.03SMESG000022832.1[more]
SMESG000022825.13.113e-625.00SMESG000022825.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004024 ID=SMED30004024|Name=SMED30004024|organism=Schmidtea mediterranea sexual|type=transcript|length=1649bp
ACAAGATTAAAGATTTATGCAAATATTTCTAAATTATCAATTTATTTGAT
GAATGATTATGATTTTTTTTCCAAAATCTCACTACAGAGTGCATTTATAT
GCCCGGTATATAACACAGCAATGCAAAATCTTGGATATCAAAGACAAAGA
AGCACTTGGACTTTGTACAGCAAACCAAGTAACGATACAATTATCGAAAA
CATTTTCAAATACTGTTTTTATTCCTACATTGTCAAAAGAAAAGAACAAC
CATATTCTGAACCGAGAAACAAGAATTTTACTAAGTCATTTGATTCCGGA
GATTACAGAAATAAGGATAGAAATACTCATTCTCCTTACAGGAATAGACA
AAATTTCCCGCAGGAAGACAGAAATCGACCACCGTTCCGAAAACCGAATC
AATGTAATTATCAGAAAAAATCATCATTTGGAGAAGAAAATCATCAACAA
AGATCAGTTGGTTTGTAAATATTCTTGCCATTAACAAATTAGCAAGCACG
CAATTATTATTTGTAAAATATAAATGAGTACAAAGATGCAACTGCAAAAC
TCAAGGTCAGTTGGAGAAATTATTTACAATTTGAATATCGAAAATCAAAA
TTTGTCTCTGGAAACCGTAACGTTTGAGTTGAATTATTTAATTTTATATT
TGAAGTACGTAATTAATTTTCTCTCACGCTGCCAATGACCTTTATAATCT
TTATTTGACCTGCTTAATTGTCGTAATTACTTGACATGCTTCCTTGGTTA
TCATGTTACCTTCTTAATCTTCCTAAATTGATGTATTTTCACAGTTGCTA
TGGTAACAGGTAGCCTACTTTATGACCTAGACAATTTTATACATCTCATT
TTTATTTTTCTATTTAATCTTCACAATAAATTGACTTACATTCATGTTTG
CCATGGTAACAACTGGCCTAATATGTGCTATAAAATTTTATATTTTACCA
TATTCATCTTAATTTTCAGTCTAAATTGACTTACTTTCATGATTACCATA
GTAACAAGAGATTTTCTTTATGGCCTACATAATTTTACACTCATTTATAT
CTTCGAACTTAATTTGCACCATGAATCAACCTTTTCACTGTCTCCATAGT
AATGTTGCGGTTATGCAAAATACTTTTTAAAAAAAGTTACAAATTATCAA
AATTAATTAAAAATTCTAAAAAGATAAAAATCAATATTTGTCGAAAGGGA
AAAGCGGTAACCGGTGACAAATGAAACAATTGTAAATTGATTAGAGATTT
ACCCAATGAAAAAAAATGCCCATAAACCAGAGCGATTCCGAGGGAACGAA
TGAATTACCGGGTTACCGCGGATTTGCACTATGGACAATAAATTGTTCGC
CAGATTTGGAAATTTTAGGCGGGAAATGATATAAATGCGCAGTCGAACCA
AACAAATCTCTAAAGTAAAAAAATCGATAATACAAAGCGAAAACTAATTC
TGTTTGCATCCAATTAGATTGTGTCGTTATTATAAACAAGTGGCTGTTCA
TTGATTCAGGGATATCTCCTTGGTTACTATATTGTGCGAAATCAAGTGTA
TTATTAATTGTGAGAGAACACGAGGAGCCAGATCGCAATCTAATTCCTAT
CGATAAATCGTTGATATCCAAATAGTTGTCTATAATTGGTTCACCTGAT
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protein sequence of SMED30004024-orf-1

>SMED30004024-orf-1 ID=SMED30004024-orf-1|Name=SMED30004024-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=112bp
SGEPIIDNYLDINDLSIGIRLRSGSSCSLTINNTLDFAQYSNQGDIPESM
NSHLFIITTQSNWMQTELVFALYYRFFYFRDLFGSTAHLYHFPPKISKSG
EQFIVHSANPR*
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protein sequence of SMED30004024-orf-2

>SMED30004024-orf-2 ID=SMED30004024-orf-2|Name=SMED30004024-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=156bp
TRLKIYANISKLSIYLMNDYDFFSKISLQSAFICPVYNTAMQNLGYQRQR
STWTLYSKPSNDTIIENIFKYCFYSYIVKRKEQPYSEPRNKNFTKSFDSG
DYRNKDRNTHSPYRNRQNFPQEDRNRPPFRKPNQCNYQKKSSFGEENHQQ
RSVGL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0003116parenchymal cell
PLANA:0007528glial cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 130..154
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 84..154
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 84..128