SMED30021176

Overview
NameSMED30021176
Smed IDSMED30021176
Length (bp)3305
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 SMED30021176 (SMED30021176) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021176 (SMED30021176) 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 SMED30021176 (SMED30021176) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021176 (SMED30021176) 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




SMED30021176

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30021176h1SMcG0002022 SmedASXL_017075SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30021176h1SMcG0002022 SmedASXL_017075SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021176 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008961:17403..21542 +16328
Homology
The following BLAST results are available for this feature:
BLAST of SMED30021176 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 SMED30021176 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 SMED30021176 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 SMED30021176 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 SMED30021176 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 SMED30021176 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 SMED30021176 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 SMED30021176 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 SMED30021176 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 SMED30021176 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 SMED30021176 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 SMED30021176 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 SMED30021176 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 SMED30021176 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

>SMED30021176 ID=SMED30021176|Name=SMED30021176|organism=Schmidtea mediterranea sexual|type=transcript|length=3305bp
TGTTTTAATATTCTTTATTTATTATGAAAGCTGAAGATCCAAAAAATTTA
GTACTTAATTTTGACATTTTCAAGCCTCACTCAAATGTGAAGGATAAAAA
TATTCCTGATTTTGCACAAAAACTCCTTGTGAAATTAGAGCAATCTTTAA
TAAAAATCCAAGATGAAACTTTAGAAAAATATATCGTTTCAAATGATGCA
GTTCTCAAATTATTAAATGAATTGGAAAATAAACTTAATTTAAACATTAA
AAAAAGTATGTTAGCCGTTAAATTGATTGATAGTTCCAAGGATATTAATC
TCGGTGAATTGTATAAATTTTCTGTAAAAAATAATGTTGTGTTGAAACGA
CATTTAAACTCCATTTATTTAACTAGTCGAATTTATAAGAAATTGTACCA
AGATCATCCATTAATGGAAAATTTAAAATTGAGATTGATTAGCGTCAGAT
GCAAAGCAATTCGGGATATATGCTTAAACGAGTCTAAGCGAGGGAAAATT
CGCCATTTGAGATGCTGGAAAAATCCGAAATTTATACCATCAACGCCAAA
GAAGTTGAAATCCATCATTAGAAAGGTTACTCGTGAATTGCAGAAATACG
CAGCGAAAGATTCGCCAATAACTCCAGTTAAAATTGATGAAATTCGTTCG
ATATTGACGAGAGATCGCAATGTCAGTTGGGATGTGATTTGCCAGAAGTT
GGAGGAAGCCATTATCAACTATTACAAAAACGTCGACTCAGATGACAGCC
AGATCGAGCAGTACACGAAAGGCCTTCAGGAAATTTGTGAAGTGCAAAAC
AAGATCGGTTATAATGCGATTCTCAATATCTGCGATGACGAGTTGGCAAT
GGAATATCTGTCAATGAAAGCCGAGGAAATCGAAGCTGATTTTAATAAAT
TGGACCCGGTATCCAATGACAACCACATCAAGCAATCGCTCGTCATTGCC
TTTGATGGAATGAAACGCGGCGTTGATTCAAATGTGAAGACTAATGTTGT
CGCTACAAAATTAGAAACCACGTCAAAATATCCTGGAAAAAAGGAAGAAG
ATCCTCAAAAAGAAGACGTGGACATGCTGGACCTGGATAATTTTCAACTT
GTTGACGTCTGGGAGGAAAAAAATGAGGAGTCTGCCAGTCAGACGGCCAA
TGAAACAGCCGGTAGTGCGGAAGGAGAAGCTGACAGAAAGGAATCTCGAC
TGGCCAGGAAGAAAAGGAGATCTCGATTTGGTCCACTGTCGGAGGAGGCG
ATGATTTTGTTACATCAGCCGAATCAATTTGGATTTTGCTCGACATTCGT
TGATGAGGAGCCGGTGAGCGATAAACACGGTGGTCAACAACATCGACCGA
TCAAAGCCACCGAATCGGTATGCACTCTGGACCCGCAATCGATCGCGGGG
GAAATTGTTGAGGACAAGCGGCCCAAAGTTGATATCAGTGCCAAAATATT
CGATGTAGTTGCACCCAGTGATGAGGTGAACCTGATAATGGAGGAGGAAG
ACCATAACCAGCACCAGCTGCAGCTGCAACATCAGCAAGAGGAAGAGACG
CCAACAACCAATGTAAAAGCTGAACAATTGCAAGCTGCCGAACCTATTTT
GGCAATGGATAAAGGCAAGCTGTGCAAGGCAATGTTGGTGAAGTTTCACG
ATTCCCTGAAACGAGCCATCGAAGGCAGCAGCAAAAAAAAAGGAAATTGG
AATGATCTGACTGAATCTATAACTGGTCAATGGGCGACTACAAGTGGCAG
TGTCAGTTGCCATCGGCCGTCCTCAGTGGCGGTTCAGTCGGTCTCCAAGG
TTGTTTATGGTGAAATCGAGAACAAAATGAACGTGCTACTGCGAGATCAC
ATGAACCGTAACCTGCTGAAACGGAAACCAATCAAAACCAGTCCGACAGT
GGTCAATGTGAATGAGAAACAGTCATCTCTTTCACCGACGGCTTTCGAGC
AAACTATTGAAGCCAGTATGAAAAAGACTCGCACAAATCCTCCTGCAGCC
ACTCCGCTTGTGGTGGGACGCCGACCGACTCGTTCCGATGGCCAATCGAG
TCCCGAACGGACTAGGCTGAGAGCGATGATGCTTTCTTACAAGCGGGACA
TCGAGAAAAGTCGGGAACGTGAAGAAAGCCATATCAGTCAAGGAGGCAGT
ACAGATGAAAGCAACTTCGTCCCGCTGGGGGAAACTGGAACCAACAAGCA
AGAACTCGTTGCTAAGGGAAAACCTCAGTTATCAGAACAGAAGATTCCCG
CTGAAACAGATTCTGAGGGCTTGCTTTCGTCCTCTGACGAGGATGATAGC
CACAACAACCGGCGGAAGGACAACAAGCAAAAGGTGCCACTCGTTACCAG
CACCCCCAAGGAAATCAAGTCGGAAAAGAATCGGATGCAGTGGCTAGTTC
ATCCTCCGGAAACGATTCCCCTAGCCCCTATTCCTGCTCCAGCTACTCCA
TTCCTGGACGAGGAATCGCAAACCTGGGCCGGCAGAAAAGTATTTGTAGT
GGATTCCCACGACAAGGGTAGCGCAATCGCCCTCATGGTGAAGGCATTTC
TCCAGAAGAACGGAGCTCGAGTCTACGATACGACCAATTACAAGACAGCT
GGTAAAGATCTCCACGTGCTCGTCCACCAAGACTGGCGGTTCCCAGACGG
TTCGAGTCGTGGGGACAATTCATCACCCAGTAGCCCCATCTCGCTCCTAC
TGCTGAAGAATAATTCCGGGGTGCATTTCCTCTCATACACGGACGTGGAG
ACGGTATCACGCTTCTCATGCCAGACCGTGTTCCCCCACAGCCGCTCGTG
CCTGTTCCTGGACCAGCACGCCCTCATCAACACCCATGCCGATAACATCC
GCAACATGCTGGAGTTCATGATCAATGAGCGGCTCACCTCCAATCGCATC
TGGTGTCTGAAGATCCCCTGTGGCGTTTACAAACTGTTCTGCGCGAAACT
GTCAGGTGAGTTCAGCGGACTGGATGCCGATAACCTGAAGGAAATCCAAT
CAATTCTCGCTGAATACTCGGCGAAATACAGCAACGATGACTCGATGTGC
CTAGTGGAAATCCAAACCGGTGAGGAGGACATCACCAATCAGCAGGAGCA
CGTGTTGAATCAGCAATATTATTTACAGAAGAAATTCAGGCATTTCTGTA
TTCTCACCGACAACTTGAACACGACTGAACTTGACATTGGATTTCTCAGC
ATTTACGGAGTGGCCGTGCTCTCCCTTAGCACCTTTCTCACCAACAAGAC
CGGGAAATACATTAAGAAGACTCCACCAGCATAATTTGACATTTTCTGTT
ACCTT
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protein sequence of SMED30021176-orf-1

>SMED30021176-orf-1 ID=SMED30021176-orf-1|Name=SMED30021176-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=1087bp
MKAEDPKNLVLNFDIFKPHSNVKDKNIPDFAQKLLVKLEQSLIKIQDETL
EKYIVSNDAVLKLLNELENKLNLNIKKSMLAVKLIDSSKDINLGELYKFS
VKNNVVLKRHLNSIYLTSRIYKKLYQDHPLMENLKLRLISVRCKAIRDIC
LNESKRGKIRHLRCWKNPKFIPSTPKKLKSIIRKVTRELQKYAAKDSPIT
PVKIDEIRSILTRDRNVSWDVICQKLEEAIINYYKNVDSDDSQIEQYTKG
LQEICEVQNKIGYNAILNICDDELAMEYLSMKAEEIEADFNKLDPVSNDN
HIKQSLVIAFDGMKRGVDSNVKTNVVATKLETTSKYPGKKEEDPQKEDVD
MLDLDNFQLVDVWEEKNEESASQTANETAGSAEGEADRKESRLARKKRRS
RFGPLSEEAMILLHQPNQFGFCSTFVDEEPVSDKHGGQQHRPIKATESVC
TLDPQSIAGEIVEDKRPKVDISAKIFDVVAPSDEVNLIMEEEDHNQHQLQ
LQHQQEEETPTTNVKAEQLQAAEPILAMDKGKLCKAMLVKFHDSLKRAIE
GSSKKKGNWNDLTESITGQWATTSGSVSCHRPSSVAVQSVSKVVYGEIEN
KMNVLLRDHMNRNLLKRKPIKTSPTVVNVNEKQSSLSPTAFEQTIEASMK
KTRTNPPAATPLVVGRRPTRSDGQSSPERTRLRAMMLSYKRDIEKSRERE
ESHISQGGSTDESNFVPLGETGTNKQELVAKGKPQLSEQKIPAETDSEGL
LSSSDEDDSHNNRRKDNKQKVPLVTSTPKEIKSEKNRMQWLVHPPETIPL
APIPAPATPFLDEESQTWAGRKVFVVDSHDKGSAIALMVKAFLQKNGARV
YDTTNYKTAGKDLHVLVHQDWRFPDGSSRGDNSSPSSPISLLLLKNNSGV
HFLSYTDVETVSRFSCQTVFPHSRSCLFLDQHALINTHADNIRNMLEFMI
NERLTSNRIWCLKIPCGVYKLFCAKLSGEFSGLDADNLKEIQSILAEYSA
KYSNDDSMCLVEIQTGEEDITNQQEHVLNQQYYLQKKFRHFCILTDNLNT
TELDIGFLSIYGVAVLSLSTFLTNKTGKYIKKTPPA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 379..399
NoneNo IPR availableCOILSCoilCoilcoord: 50..70
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 684..706
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 366..400
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 753..770
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 731..780
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 648..717