SMED30008762

Overview
NameSMED30008762
Smed IDSMED30008762
Length (bp)579
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 SMED30008762 (SMED30008762) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008762 (SMED30008762) 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 SMED30008762 (SMED30008762) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008762 (SMED30008762) 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




SMED30008762

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
intestinal phagocyteSMED30008762SMESG000020876.1 Contig1571GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30008762SMESG000006038.1 SMESG000005903.1 SMESG000005899.1 SMESG000005759.1 SMESG000005757.1 Contig1571GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pigment cellSMED30008762SMESG000006038.1 SMESG000005903.1 SmedASXL_014890SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017
whole organism asexual adult RNA-sequencing evidence
gutSMED30008762SMESG000006038.1 SMESG000005903.1 dd_Smed_v4_1785_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30008762SMESG000006038.1 SMESG000005903.1 dd_Smed_v4_1785_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30008762 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000610:55608..56230 -2823
v31.001923:26486..27113 +2474
v31.001923:540..1167 -2456
v31.003456:25444..26080 -2242
Homology
BLAST of SMED30008762 vs. TrEMBL
Match: I1ZIH8 (Uncharacterized protein (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 284.648 bits (727), Expect = 7.844e-96
Identity = 138/153 (90.20%), Postives = 144/153 (94.12%), Query Frame = 3
Query:   75 KIKLLNYQTNDCVFVNANKSVGIQKKNPIQNSSNLYISFLPNDWSFPFIICKIKHFSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIVVGNSGQFCLCQSDESSLDGHFTLICEENSKLVTEKYEGNLNIIKSDWIADRKKSQYFWYPWS 533
            +IKL NYQT+DCVFVNANKSVGIQKKNP QNSSNLYISFLPNDWSFP+I CKIKH STQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFI+VGNSGQFCLCQSDESSLDGHF LICEENSKLVTEKYEGNLNIIK+ WI +R KSQYFW PWS
Sbjct:    1 QIKLFNYQTDDCVFVNANKSVGIQKKNPFQNSSNLYISFLPNDWSFPWITCKIKHCSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIIVGNSGQFCLCQSDESSLDGHFKLICEENSKLVTEKYEGNLNIIKNVWIGNRNKSQYFWSPWS 153          
BLAST of SMED30008762 vs. Planmine SMEST
Match: SMESG000006038.1 (SMESG000006038.1)

HSP 1 Score: 329.717 bits (844), Expect = 2.950e-117
Identity = 160/160 (100.00%), Postives = 160/160 (100.00%), Query Frame = 3
Query:   69 MGKIKLLNYQTNDCVFVNANKSVGIQKKNPIQNSSNLYISFLPNDWSFPFIICKIKHFSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIVVGNSGQFCLCQSDESSLDGHFTLICEENSKLVTEKYEGNLNIIKSDWIADRKKSQYFWYPWSLTDGF 548
            MGKIKLLNYQTNDCVFVNANKSVGIQKKNPIQNSSNLYISFLPNDWSFPFIICKIKHFSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIVVGNSGQFCLCQSDESSLDGHFTLICEENSKLVTEKYEGNLNIIKSDWIADRKKSQYFWYPWSLTDGF
Sbjct:    1 MGKIKLLNYQTNDCVFVNANKSVGIQKKNPIQNSSNLYISFLPNDWSFPFIICKIKHFSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIVVGNSGQFCLCQSDESSLDGHFTLICEENSKLVTEKYEGNLNIIKSDWIADRKKSQYFWYPWSLTDGF 160          
BLAST of SMED30008762 vs. Planmine SMEST
Match: SMESG000005903.1 (SMESG000005903.1)

HSP 1 Score: 287.73 bits (735), Expect = 1.380e-100
Identity = 139/155 (89.68%), Postives = 145/155 (93.55%), Query Frame = 3
Query:   69 MGKIKLLNYQTNDCVFVNANKSVGIQKKNPIQNSSNLYISFLPNDWSFPFIICKIKHFSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIVVGNSGQFCLCQSDESSLDGHFTLICEENSKLVTEKYEGNLNIIKSDWIADRKKSQYFWYPWS 533
            M +IKL NYQT+DCVFVNANKSVGIQKKNP QNSSNLYISFLPNDWSFP+I CKIKH STQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFI+VGNSGQFCLCQSDESSLDGHF LICEENSKLVTEKYEGNLNIIK+ WI +R KSQYFW PWS
Sbjct:    1 MSQIKLFNYQTDDCVFVNANKSVGIQKKNPFQNSSNLYISFLPNDWSFPWITCKIKHCSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIIVGNSGQFCLCQSDESSLDGHFKLICEENSKLVTEKYEGNLNIIKNVWIGNRNKSQYFWSPWS 155          
BLAST of SMED30008762 vs. Planmine SMEST
Match: SMESG000005899.1 (SMESG000005899.1)

HSP 1 Score: 287.73 bits (735), Expect = 1.380e-100
Identity = 139/155 (89.68%), Postives = 145/155 (93.55%), Query Frame = 3
Query:   69 MGKIKLLNYQTNDCVFVNANKSVGIQKKNPIQNSSNLYISFLPNDWSFPFIICKIKHFSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIVVGNSGQFCLCQSDESSLDGHFTLICEENSKLVTEKYEGNLNIIKSDWIADRKKSQYFWYPWS 533
            M +IKL NYQT+DCVFVNANKSVGIQKKNP QNSSNLYISFLPNDWSFP+I CKIKH STQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFI+VGNSGQFCLCQSDESSLDGHF LICEENSKLVTEKYEGNLNIIK+ WI +R KSQYFW PWS
Sbjct:    1 MSQIKLFNYQTDDCVFVNANKSVGIQKKNPFQNSSNLYISFLPNDWSFPWITCKIKHCSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIIVGNSGQFCLCQSDESSLDGHFKLICEENSKLVTEKYEGNLNIIKNVWIGNRNKSQYFWSPWS 155          
BLAST of SMED30008762 vs. Planmine SMEST
Match: SMESG000005759.1 (SMESG000005759.1)

HSP 1 Score: 267.7 bits (683), Expect = 9.473e-93
Identity = 131/155 (84.52%), Postives = 139/155 (89.68%), Query Frame = 3
Query:   69 MGKIKLLNYQTNDCVFVNANKSVGIQKKNPIQNSSNLYISFLPNDWSFPFIICKIKHFSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIVVGNSGQFCLCQSDESSLDGHFTLICEENSKLVTEKYEGNLNIIKSDWIADRKKSQYFWYPWS 533
            M  IKL NYQTND V VN+NKSV +QKKNPIQ+SSNL+ISFLPNDWSFP+I C+IKH STQMYFCKSRFNRGFSLTDDKS IK LNDPRCFI VGNSGQFCLCQSDESSLD HF LICE+NSKLVT KYEGNLNIIKSDWI +RKKSQYFWY WS
Sbjct:    1 MSTIKLFNYQTNDYVHVNSNKSVDVQKKNPIQDSSNLFISFLPNDWSFPWITCEIKHCSTQMYFCKSRFNRGFSLTDDKSVIKNLNDPRCFIFVGNSGQFCLCQSDESSLDNHFKLICEKNSKLVTVKYEGNLNIIKSDWIGNRKKSQYFWYTWS 155          
BLAST of SMED30008762 vs. Planmine SMEST
Match: SMESG000005757.1 (SMESG000005757.1)

HSP 1 Score: 267.7 bits (683), Expect = 9.473e-93
Identity = 131/155 (84.52%), Postives = 139/155 (89.68%), Query Frame = 3
Query:   69 MGKIKLLNYQTNDCVFVNANKSVGIQKKNPIQNSSNLYISFLPNDWSFPFIICKIKHFSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIVVGNSGQFCLCQSDESSLDGHFTLICEENSKLVTEKYEGNLNIIKSDWIADRKKSQYFWYPWS 533
            M  IKL NYQTND V VN+NKSV +QKKNPIQ+SSNL+ISFLPNDWSFP+I C+IKH STQMYFCKSRFNRGFSLTDDKS IK LNDPRCFI VGNSGQFCLCQSDESSLD HF LICE+NSKLVT KYEGNLNIIKSDWI +RKKSQYFWY WS
Sbjct:    1 MSTIKLFNYQTNDYVHVNSNKSVDVQKKNPIQDSSNLFISFLPNDWSFPWITCEIKHCSTQMYFCKSRFNRGFSLTDDKSVIKNLNDPRCFIFVGNSGQFCLCQSDESSLDNHFKLICEKNSKLVTVKYEGNLNIIKSDWIGNRKKSQYFWYTWS 155          
The following BLAST results are available for this feature:
BLAST of SMED30008762 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 SMED30008762 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 SMED30008762 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 SMED30008762 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 SMED30008762 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 SMED30008762 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 SMED30008762 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 SMED30008762 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZIH87.844e-9690.20Uncharacterized protein (Fragment) OS=Schmidtea me... [more]
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BLAST of SMED30008762 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 SMED30008762 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 SMED30008762 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 SMED30008762 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 SMED30008762 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 SMED30008762 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000006038.12.950e-117100.00SMESG000006038.1[more]
SMESG000005903.11.380e-10089.68SMESG000005903.1[more]
SMESG000005899.11.380e-10089.68SMESG000005899.1[more]
SMESG000005759.19.473e-9384.52SMESG000005759.1[more]
SMESG000005757.19.473e-9384.52SMESG000005757.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008762 ID=SMED30008762|Name=SMED30008762|organism=Schmidtea mediterranea sexual|type=transcript|length=579bp
TCAACTTAAGCTCTATATAAACTGATCTGATTGATAATAATTTCATTTAA
TAAATTTTATTTGTTTTAATGGGGAAAATCAAATTATTAAATTATCAAAC
CAATGACTGCGTTTTTGTCAACGCCAATAAGTCTGTTGGCATACAGAAAA
AGAATCCGATTCAAAACTCATCAAATTTGTACATTAGTTTCCTTCCAAAC
GACTGGAGCTTCCCTTTTATCATTTGCAAGATAAAGCATTTTTCCACTCA
AATGTATTTCTGTAAATCTAGATTCAACCGAGGATTTAGTCTGACTGATG
ACAAATCTGACATCAAAAGATTGAATGATCCCAGATGTTTCATTGTTGTT
GGTAACTCTGGCCAATTCTGTCTATGTCAGTCAGATGAGTCTAGCTTGGA
CGGCCACTTCACACTAATTTGTGAGGAAAACAGCAAACTTGTTACAGAGA
AATATGAAGGAAATCTCAATATTATAAAAAGTGATTGGATTGCAGATCGG
AAAAAATCTCAATATTTTTGGTATCCTTGGAGTTTGACAGATGGCTTTTA
ATATATTATTTAATCTTTATCAAAAAAAA
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protein sequence of SMED30008762-orf-1

>SMED30008762-orf-1 ID=SMED30008762-orf-1|Name=SMED30008762-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=161bp
MGKIKLLNYQTNDCVFVNANKSVGIQKKNPIQNSSNLYISFLPNDWSFPF
IICKIKHFSTQMYFCKSRFNRGFSLTDDKSDIKRLNDPRCFIVVGNSGQF
CLCQSDESSLDGHFTLICEENSKLVTEKYEGNLNIIKSDWIADRKKSQYF
WYPWSLTDGF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0002075pigment cell
PLANA:0003116parenchymal cell