SMED30009888

Overview
NameSMED30009888
Smed IDSMED30009888
Length (bp)1636
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 SMED30009888 (SMED30009888) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009888 (SMED30009888) 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 SMED30009888 (SMED30009888) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009888 (SMED30009888) 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



SMED30009888

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
ovarySMED30009888SMESG000035929.1 Contig1230newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009888 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000630:29004..30679 +7876
Homology
[Close]
BLAST of SMED30009888 vs. Planmine SMEST
Match: SMESG000026733.1 (SMESG000026733.1)

HSP 1 Score: 90.1225 bits (222), Expect = 7.932e-30
Identity = 46/94 (48.94%), Postives = 58/94 (61.70%), Query Frame = 2 
Query: 1244 FFLYRLEELGPKFHSKVVMANIHLNRVNTAITIGETPSTSGYAPEYDVFFELNDPVLNRMSAPTSVVLPAKIFNGPIRSRLSNRREDDDHSYHC 1525
            F LYRLEEL  KF  KV M   HL ++N  I  GE PST GYA +Y + FELNDPVL +M   T+ +LPA++FN  IR ++ + R      Y C
Sbjct:   78 FSLYRLEELVRKFQWKVRMTQRHLKQINATIATGEIPSTDGYAQDYGLLFELNDPVLTQMH--TNAILPAQLFNERIRHQIVDWR------YEC 163

HSP 2 Score: 60.077 bits (144), Expect = 7.932e-30
Identity = 35/68 (51.47%), Postives = 44/68 (64.71%), Query Frame = 1 
Query: 1030 WKDKDLETIRMAPGMTAKCRQSFWDARYSLVTIRENS*MENRTNSRDDEKDLPSLAIKRKLG*NSARE 1233
            W D+D  TI++ P M A+ RQS WD  YSL T+ +NS    R  SRD+E +L SLAIKR+   N ARE
Sbjct:    5 WCDEDRVTIKVTPDMAAQYRQSLWDVSYSLATLGDNS-WPIRDKSRDNEIELLSLAIKREPDRNLARE 71
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BLAST of SMED30009888 vs. Planmine SMEST
Match: SMESG000020573.1 (SMESG000020573.1)

HSP 1 Score: 104.375 bits (259), Expect = 1.126e-26
Identity = 50/87 (57.47%), Postives = 62/87 (71.26%), Query Frame = 2 
Query: 1253 YRLEELGPKFHSKVVMANIHLNRVNTAITIGETPSTSGYAPEYDVFFELNDPVLNRMSAPTSVVLPAKIFNGPIRSRLSNRREDDDH 1513
            YRL+++  KFH K  M+   + R N +I  GE PST GYAPEY VF EL+DP L+RM APTSVVL A++F GP+ SR+ NRRE  DH
Sbjct:    4 YRLKKIEWKFHWKTAMSRRRVMRFNESIVAGEIPSTDGYAPEYGVFSELDDPALDRMDAPTSVVLSARMFRGPVHSRVGNRRERGDH 90
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BLAST of SMED30009888 vs. Planmine SMEST
Match: SMESG000027782.1 (SMESG000027782.1)

HSP 1 Score: 92.8189 bits (229), Expect = 1.447e-26
Identity = 45/97 (46.39%), Postives = 62/97 (63.92%), Query Frame = 2 
Query: 1244 FFLYRLEELGPKFHSKVVMANIHLNRVNTAITIGETPSTSGYAPEYDVFFELNDPVLNRMSAPTSVVLPAKIFNGPIRSRLSNRREDDDHSYHCRHP 1534
            +   ++EEL  K+H K V+A   L +VN  I  G  PST G+ PEY V FEL+DP L +M+APT +VLP K+    +R+RL + R+  DH+Y  RHP
Sbjct:  109 YAAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKLVLPEKLIQSTLRNRLGS-RQTGDHTYASRHP 204

HSP 2 Score: 46.595 bits (109), Expect = 1.447e-26
Identity = 27/70 (38.57%), Postives = 40/70 (57.14%), Query Frame = 1 
Query: 1027 TWKDKDLETIRMAPGMTAKCRQSFWDARYSLVTIRENS*MENRTNSRDDEKDLPSLAIKRKLG*NSAREA 1236
            +W D    T+++     A+ RQ  WD  Y L T  ++S    R+  + +E +LPS+AIKR+ G N AREA
Sbjct:   35 SWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSS-WPRRSKYQAEEIELPSIAIKREPGHNPAREA 103
[Close]
BLAST of SMED30009888 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 89.7373 bits (221), Expect = 5.628e-26
Identity = 44/93 (47.31%), Postives = 61/93 (65.59%), Query Frame = 2 
Query: 1256 RLEELGPKFHSKVVMANIHLNRVNTAITIGETPSTSGYAPEYDVFFELNDPVLNRMSAPTSVVLPAKIFNGPIRSRLSNRREDDDHSYHCRHP 1534
            ++EEL  K+H K V+A   L +VN  I  G  PST G+ PEY V FEL+DP L +M+APT +V+P K+    +R+RL + R+  DH+Y  RHP
Sbjct: 1213 KMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGS-RQTGDHTYASRHP 1304

HSP 2 Score: 47.7506 bits (112), Expect = 5.628e-26
Identity = 29/78 (37.18%), Postives = 41/78 (52.56%), Query Frame = 1 
Query: 1003 DVRPQEADTWKDKDLETIRMAPGMTAKCRQSFWDARYSLVTIRENS*MENRTNSRDDEKDLPSLAIKRKLG*NSAREA 1236
            D R      W D    T+++     A+ RQ  WD  Y L T  ++S    R+  + +E +LPS+AIKR+ G N AREA
Sbjct: 1127 DNRRDPHGNWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSS-WPRRSEYQAEEIELPSIAIKREPGHNPAREA 1203
[Close]
BLAST of SMED30009888 vs. Planmine SMEST
Match: SMESG000042475.1 (SMESG000042475.1)

HSP 1 Score: 88.5817 bits (218), Expect = 8.200e-26
Identity = 44/93 (47.31%), Postives = 60/93 (64.52%), Query Frame = 2 
Query: 1256 RLEELGPKFHSKVVMANIHLNRVNTAITIGETPSTSGYAPEYDVFFELNDPVLNRMSAPTSVVLPAKIFNGPIRSRLSNRREDDDHSYHCRHP 1534
            ++EEL  K+H K V+A   L +VN  I  G  PST G+  EY V FEL+DP L +M+APT +VLP K+    +R+RL + R+  DH+Y  RHP
Sbjct: 1408 KMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPQEYGVSFELDDPRLMQMTAPTKLVLPEKLIQSTLRNRLGS-RQTGDHTYASRHP 1499

HSP 2 Score: 48.1358 bits (113), Expect = 8.200e-26
Identity = 28/78 (35.90%), Postives = 43/78 (55.13%), Query Frame = 1 
Query: 1003 DVRPQEADTWKDKDLETIRMAPGMTAKCRQSFWDARYSLVTIRENS*MENRTNSRDDEKDLPSLAIKRKLG*NSAREA 1236
            + R   + +W D    T+++     A+ RQ  WD  Y L T  ++S    R+  + +E +LPS+AIKR+ G N AREA
Sbjct: 1322 EYRRDTSGSWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSS-WPRRSEYQAEEIELPSIAIKREPGHNPAREA 1398
The following BLAST results are available for this feature:
BLAST of SMED30009888 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 SMED30009888 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 SMED30009888 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 SMED30009888 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 SMED30009888 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 SMED30009888 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 SMED30009888 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 SMED30009888 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 SMED30009888 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 SMED30009888 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 SMED30009888 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 SMED30009888 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 SMED30009888 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 SMED30009888 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000026733.17.932e-3048.94SMESG000026733.1[more]
SMESG000020573.11.126e-2657.47SMESG000020573.1[more]
SMESG000027782.11.447e-2646.39SMESG000027782.1[more]
SMESG000044971.15.628e-2647.31SMESG000044971.1[more]
SMESG000042475.18.200e-2647.31SMESG000042475.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009888 ID=SMED30009888|Name=SMED30009888|organism=Schmidtea mediterranea sexual|type=transcript|length=1636bp
TTTAAACACAGACAAATTCACCCAAGCAGCTAAGTAGCCAGACAATTATC
AATGATTATTTGCGAATCTGACCTGATATGAAGTGCAGAGAGAAATCGGA
TTTTCTAAACTTAAGGTCAGCGAATTATGAATATAAATCATCGGATTACC
GCCAATACGATTTGATGTCAGCTAATTATGGAAATAAAGCATCGACTAAA
AGAAAACAAATAATAATAATTATTTGAGGTAAGGCATGACTCACCCAAGC
TAGGAGTATGTGTAATTCTTTGTTTAAATGACATATTCATTTAACACGCT
CTAATGAAAACACAAAACAAATCAAGTCCTTCCGACTGTAAGGAGGCTGT
CGGAGGACCTTCAAGCAGGGCAAGTCAAAGTACTGACCCAGAGGATCAGG
ATCCTACAACGAAGCAAATTTCGGGCACGTCTGACGAAAATGATCAAACT
CCCCATAATCATATAGTAATCAAATTACACTAAAAATGAGGAAATAGGAA
CAACCAATCGTTCACCAGCGGATAATGGTGAAGAGAAACCCTTCGCCAAC
CTTGCTGTTAGTTCATTTATCAACAGGACTGAAAGCAAATACAATAAGTG
TTGAACTCTAGATTATTGTTATCAGTTCCCACCGAAATCCGTTAGACCAA
AAGTGAGAAACAGTCTGCGTAAGATTCCATTAATGAAATCACAGACCTTC
AATCTAGTAATATAATTAATTGAGTTTACAAACGGTCAATTTTATATTAT
ATATTTGTGCTGTAACGTATTTTAGACTTTAGGTAATATTGACTCCCAAC
TACCGCATTTAAATTGGTCAAAGAAATAGAGAAAAACACATAAACACGAC
TAACGGAAATCACAAATACTAGTACTTATTAGATTTTTTTTAATTTGGTT
GTCAATCTGGTGAGTTGAAGCTATGTTTATTCACATATATTTATAGTCTA
TTTCAACTTATATTCCAGATAATGTAATTAGTATTTATTCTACATTTTAG
CTGATGTTAGACCTCAGGAGGCAGACACGTGGAAAGACAAGGATCTAGAG
ACGATAAGAATGGCTCCAGGAATGACAGCGAAATGCAGACAATCGTTTTG
GGATGCTCGATACAGCTTGGTTACAATCAGAGAAAACAGTTAAATGGAAA
ATCGCACAAATTCTAGAGATGATGAAAAAGATCTACCGAGCCTAGCCATA
AAACGCAAGCTTGGCTGAAACTCGGCCCGCGAGGCCGCTATAGTTCTTTC
TATATCGGTTGGAGGAATTGGGACCCAAATTCCACTCGAAAGTGGTAATG
GCTAATATTCACCTGAACCGCGTCAATACAGCGATAACCATTGGAGAAAC
ACCCAGTACCAGCGGCTATGCGCCGGAGTATGACGTCTTCTTCGAGCTCA
ATGATCCAGTACTAAACCGGATGAGTGCGCCTACCAGTGTGGTACTCCCA
GCAAAGATATTCAATGGTCCAATTCGAAGTCGATTGAGCAACAGAAGAGA
AGATGACGATCACTCGTACCACTGCCGACATCCAATGAAAATAACCAAGG
TGATCATATGCATCATCCAATCCCAGCCACCGAGGAGGACCATACTAAAG
AGCGGTTCTAGCATTTCTATTAGTGAGATCGGAAGA
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