SMED30011226

Overview
NameSMED30011226
Smed IDSMED30011226
Length (bp)1424
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 SMED30011226 (SMED30011226) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011226 (SMED30011226) 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.
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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




SMED30011226

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
X2 cellSMED30011226 SmedASXL_022048SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30011226 SmedASXL_079422SmedAsxl_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
SMED30011226 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006532:25985..27520 +6930
Homology
BLAST of SMED30011226 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 72.4034 bits (176), Expect = 7.329e-20
Identity = 49/127 (38.58%), Postives = 71/127 (55.91%), Query Frame = -3
Query:  349 PWKISSSLKLKKFE*IFITTHNLSSCIHDVYFPIDTREFTTG*AWQDEYRIIIDVAAPNAAQYRQALWDHRYVISTMGDPEWPMHXXXXXXXXXXXXXXIKIEPGRNPAQKIQQKA*YILAKSEEAE 729
            P K+   LK + F+ +FI T             ID R+   G  W+D+ +I + ++  +AA+YRQALWD+ Y +ST G+  WP   + R     + SI IK EPGRNPA+++ Q+A Y   K EE E
Sbjct:  644 PSKMYDILK-EDFDYVFIAT-----------VTIDRRDPHGG--WRDDSQITLQISNASAARYRQALWDNGYTLSTYGESSWPRRPKDREDEVELPSIAIKREPGRNPAREVHQRAEYTSMKMEEME 756          

HSP 2 Score: 44.2838 bits (103), Expect = 7.329e-20
Identity = 23/42 (54.76%), Postives = 26/42 (61.90%), Query Frame = -1
Query:  219 KTSTARRHLAWINEEIASGRIPSPYEHQPTYGVSHRQNDPAL 344
            K   AR+ LA IN +IASG IPS     PTYGVS   +DP L
Sbjct:  762 KAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRL 803          
BLAST of SMED30011226 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 72.0182 bits (175), Expect = 7.699e-20
Identity = 49/127 (38.58%), Postives = 71/127 (55.91%), Query Frame = -3
Query:  349 PWKISSSLKLKKFE*IFITTHNLSSCIHDVYFPIDTREFTTG*AWQDEYRIIIDVAAPNAAQYRQALWDHRYVISTMGDPEWPMHXXXXXXXXXXXXXXIKIEPGRNPAQKIQQKA*YILAKSEEAE 729
            P K+   LK + F+ +FI T             ID R+   G  W+D+ +I + ++  +AA+YRQALWD+ Y +ST G+  WP   + R     + SI IK EPGRNPA+++ Q+A Y   K EE E
Sbjct:  640 PSKMYDILK-EDFDYVFIAT-----------VTIDRRDPHGG--WRDDSQITLQISNASAARYRQALWDNGYTLSTYGESSWPRRPKDREDEVELPSIAIKREPGRNPAREVHQRAEYTSMKMEEME 752          

HSP 2 Score: 44.2838 bits (103), Expect = 7.699e-20
Identity = 23/42 (54.76%), Postives = 26/42 (61.90%), Query Frame = -1
Query:  219 KTSTARRHLAWINEEIASGRIPSPYEHQPTYGVSHRQNDPAL 344
            K   AR+ LA IN +IASG IPS     PTYGVS   +DP L
Sbjct:  758 KAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRL 799          
BLAST of SMED30011226 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 74.7146 bits (182), Expect = 8.427e-20
Identity = 35/83 (42.17%), Postives = 52/83 (62.65%), Query Frame = -3
Query:  349 WQDEYRIIIDVAAPNAAQYRQALWDHRYVISTMGDPEWPMHXXXXXXXXXXXXXXIKIEPGRNPAQKIQQKA*YILAKSEEAE 597
            W D  R+ + + + +AA+YRQ LWD+ Y++ST GD  WP   + +     + SI IK EPG NPA++ +Q+A Y+  K EE E
Sbjct: 1136 WSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAEYVAMKMEELE 1218          

HSP 2 Score: 41.5874 bits (96), Expect = 8.427e-20
Identity = 21/42 (50.00%), Postives = 25/42 (59.52%), Query Frame = -1
Query:  219 KTSTARRHLAWINEEIASGRIPSPYEHQPTYGVSHRQNDPAL 344
            K   AR+ LA +N +IASG IPS     P YGVS   +DP L
Sbjct: 1224 KAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRL 1265          
BLAST of SMED30011226 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 68.9366 bits (167), Expect = 7.353e-19
Identity = 37/84 (44.05%), Postives = 54/84 (64.29%), Query Frame = -3
Query:  349 AWQDEYRIIIDVAAPNAAQYRQALWDHRYVISTMGDPEWPMHXXXXXXXXXXXXXXIKIEPGRNPAQKIQQKA*YILAKSEEAE 600
             W+D+ +I + ++  +AA+YRQALWD+ Y +ST G+  WP   + R     + SI IK EPGRNPA+++ Q+A Y   K EE E
Sbjct:  617 GWRDDSQITLQISNASAARYRQALWDNGYTLSTYGESSWPRRPKDREDEVELPSIAIKREPGRNPAREVHQRAEYTSMKMEEME 700          

HSP 2 Score: 43.8986 bits (102), Expect = 7.353e-19
Identity = 23/42 (54.76%), Postives = 26/42 (61.90%), Query Frame = -1
Query:  219 KTSTARRHLAWINEEIASGRIPSPYEHQPTYGVSHRQNDPAL 344
            K   AR+ LA IN +IASG IPS     PTYGVS   +DP L
Sbjct:  706 KAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRL 747          
BLAST of SMED30011226 vs. Planmine SMEST
Match: SMESG000052862.1 (SMESG000052862.1)

HSP 1 Score: 70.8626 bits (172), Expect = 1.516e-18
Identity = 34/84 (40.48%), Postives = 54/84 (64.29%), Query Frame = -3
Query:  349 AWQDEYRIIIDVAAPNAAQYRQALWDHRYVISTMGDPEWPMHXXXXXXXXXXXXXXIKIEPGRNPAQKIQQKA*YILAKSEEAE 600
            +W D  R+ + + + +AA+YRQ LWD+ Y++ST GD  WP   +S+     + SI+I  EPG+NPA++ +Q+A +   K EE E
Sbjct: 2102 SWNDNSRVTLQIPSASAARYRQMLWDNGYLLSTYGDSSWPRRSESQAEEIELPSIVINREPGKNPAREARQRAEFTAMKMEELE 2185          

HSP 2 Score: 41.2022 bits (95), Expect = 1.516e-18
Identity = 23/56 (41.07%), Postives = 30/56 (53.57%), Query Frame = -1
Query:  177 KTSTARRHLAWINEEIASGRIPSPYEHQPTYGVSHRQNDPALRR*MLQPVSRCQIE 344
            K   AR+ L  +N +IASG IPS     P YGVS   +DP L++ M  P     +E
Sbjct: 2191 KAVLARQRLVQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLKQ-MTTPTKLVLLE 2245          
The following BLAST results are available for this feature:
BLAST of SMED30011226 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 SMED30011226 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 SMED30011226 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 SMED30011226 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 SMED30011226 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 SMED30011226 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 SMED30011226 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 SMED30011226 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 SMED30011226 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 SMED30011226 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 SMED30011226 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 SMED30011226 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 SMED30011226 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 SMED30011226 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046313.17.329e-2038.58SMESG000046313.1[more]
SMESG000046313.17.699e-2038.58SMESG000046313.1[more]
SMESG000044971.18.427e-2042.17SMESG000044971.1[more]
SMESG000046313.17.353e-1944.05SMESG000046313.1[more]
SMESG000052862.11.516e-1840.48SMESG000052862.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011226 ID=SMED30011226|Name=SMED30011226|organism=Schmidtea mediterranea sexual|type=transcript|length=1424bp
TTTATTTATTTNNTCTNCNNATNNNCAAAAATATTATTCGGATACACATA
GGTGGAATAGATCATCCGCCAGTCAAGTTTCAGTTTGTTCGCTTCCCACG
TCGTTCAAAGCTGCATCCCGGTATTTTCCTTTGTCAGGCCATCTTTGAAA
TTGTCTCCTGAGTGCAGGAATTAGAACTCTATTTGGCACCGCGATACGGG
TTGGAGCATTTATCGTCGTAGAGCCGGATCATTTTGGCGATGTGAGACGC
CGTATGTTGGTTGATGCTCGTATGGGCTCGGAATACGCCCTGACGCTATC
TCTTCATTTATCCAAGCGAGGTGACGTCTAGCTGTCGACGTCTTCCATCT
CGGCCTCTTCGGATTTGGCCAATATATATTAAGCTTTTTGTTGTATTTTT
TGAGCCGGATTTCTTCCTGGCTCTATCTTAATGATAATACTGGACACATT
GCTGTTCCTGTTTCTTGATTGCCGGTGCATGGGCCATTCCGGGTCACCCA
TAGTAGATATCACATAGCGGTGATCCCAGAGCGCCTGTCGATATTGCGCT
GCGTTTGGGGCGGCCACATCGATGATGATCCTGTATTCATCCTGCCAAGC
TTATCCGGTGGTAAATTCTCTGGTATCTATTGGAAAGTAAACATCATGAA
TGCATGAACTTAGATTATGAGTAGTAATAAATATTTATTCGAATTTCTTC
AATTTCAACGACGAGGATATTTTCCATGGATAATTAATCATTATGATAGA
ACTATCATTTTTTCCTTGTTACGGTAGTTTACCATCCATATATATTTATA
AGTATAAATGTAAATCATCGTGTCTCGAGGAGCCCGATCTTCTTGGTTCT
CCTCGTAAATGTTAGAGTCGTGTCGTTGACGTCTAGTTACCGGCATAATT
TCGTACTCCGAGTGCATCAAGTGTGATTTCTGTGGCCTCATTGGTAACAT
TCTTTCTTATTGATTTGACGTAATTGTGAACAAATTCTCTAACCTGATTG
CTTCTTATATGATCCATGAACATTGGAGCGGATTGATCACAACACTACAC
TATATAATTTTATGAATTGAAATTTTTGACTGGACGCTTCAGTACATTTA
TTCAAATGACTAGTTTGACTTCAATTGATATATCTTATTTTATTAGTCAT
ATGTGGGTGATTCACGTTAGCGTGAATCATTATTAACCATAATATTGCTA
ACAATGATTAACTAGTGACTGCATTGATGAGGTCCTGTCGCTTCTCTCCA
GATCTACGTCCCTATTGAATTGGGAAATGCTGAGTTCAACTGTTTGAAGT
GGGAGGGTTAAATTACTCCACCAAAGTACTTTGGTATCTCTCCGCCACTA
TGGTTCGATTTCTTAGTATAATTGGGTGTCATTCGATGTTAAATGTTTCT
GTGATACTACCTATATCCCGAAAT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell