SMED30026519

Overview
NameSMED30026519
Smed IDSMED30026519
Length (bp)1160
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 SMED30026519 (SMED30026519) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026519 (SMED30026519) 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 SMED30026519 (SMED30026519) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026519 (SMED30026519) 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



SMED30026519

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



PAGE Curations: 27

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30026519h1SMcG0009890 SmedASXL_004369SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30026519h1SMcG0009890 SmedASXL_017252SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30026519h1SMcG0009890 SmedASXL_017257SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30026519h1SMcG0009890 dd_Smed_v4_13603_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026519h1SMcG0009890 dd_Smed_v4_13603_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30026519h1SMcG0009890 dd_Smed_v4_13603_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30026519h1SMcG0009890 dd_Smed_v4_11640_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026519h1SMcG0009890 dd_Smed_v4_11640_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30026519h1SMcG0009890 dd_Smed_v4_9830_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30026519h1SMcG0009890 dd_Smed_v4_9830_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026519h1SMcG0009890 dd_Smed_v4_9830_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30026519h1SMcG0009890 dd_Smed_v4_9830_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30026519h1SMcG0009890 dd_Smed_v4_9830_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30026519h1SMcG0009890 dd_Smed_v4_9830_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30026519h1SMcG0009890 dd_Smed_v4_16650_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026519h1SMcG0009890 dd_Smed_v4_16650_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30026519h1SMcG0009890 dd_Smed_v4_16650_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026519h1SMcG0009889 Contig19558uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026519h1SMcG0009889 Contig19558newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026519h1SMcG0009890 Contig53784uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026519h1SMcG0009890 Contig53784newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026519h1SMcG0009890 Contig19558uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026519h1SMcG0009890 Contig19558newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30026519h1SMcG0009890 dd_Smed_v6_9830_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
neoblastSMED30026519h1SMcG0009890 dd_Smed_v6_16650_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30026519h1SMcG0009890 Contig53784uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30026519h1SMcG0009890 Contig53784newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30026519 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000055:320279..321400 -5317
Homology
[Close]
BLAST of SMED30026519 vs. Planmine SMEST
Match: SMESG000064314.1 (SMESG000064314.1)

HSP 1 Score: 304.679 bits (779), Expect = 2.928e-170
Identity = 159/161 (98.76%), Postives = 160/161 (99.38%), Query Frame = -2 
Query:  284 HNPLEFDLVDIQKNKDLEKNSENDNVNVEIQNLQETNKQITVDEIKESNSASLEPAEKGIEEHIKETSKKSENDEDMSKIIISLNKVDNKAIISNNLKEIQNVDDSDKEKTCNLEIIKDALEAHDTRENKDQETSNGNSSKMSPDAEQFEVIDYSEEILLD 766
             NPLEFDLVDIQKNKDLEKNSENDNVNVEIQNLQETNKQITVDEIKESNSASLEPAEKGIEEHIKETSKKSENDEDMSKIIISLNKVDNKAIISNNLKEIQNVDDSDKEKTCNLEIIKDALEAHDTRENKDQETSNGNSSKMSPDAEQFEVIDYSEEILL+
Sbjct:  605 RNPLEFDLVDIQKNKDLEKNSENDNVNVEIQNLQETNKQITVDEIKESNSASLEPAEKGIEEHIKETSKKSENDEDMSKIIISLNKVDNKAIISNNLKEIQNVDDSDKEKTCNLEIIKDALEAHDTRENKDQETSNGNSSKMSPDAEQFEVIDYSEEILLE 765

HSP 2 Score: 151.754 bits (382), Expect = 2.928e-170
Identity = 76/78 (97.44%), Postives = 76/78 (97.44%), Query Frame = -1 
Query:  765 KKIGLEEINKIKQIKVTKEVPENIKPVECKSKEISSDNITNEDTLTNIGSMEILGGVEEFAYVSDLDVNKTETTERNP 998
            KKIGLEEINKIKQIKVTKE PENIKPVECKSKEISSDNITNEDTLTNIGSMEILGGVEEF YVSDLDVNKTETTERNP
Sbjct:  530 KKIGLEEINKIKQIKVTKEFPENIKPVECKSKEISSDNITNEDTLTNIGSMEILGGVEEFTYVSDLDVNKTETTERNP 607

HSP 3 Score: 129.413 bits (324), Expect = 2.928e-170
Identity = 79/96 (82.29%), Postives = 83/96 (86.46%), Query Frame = -3 
Query:    1 LILETKIKNVNITQVSSKSSDENMNNSEHIERISDQNAEEDQMXXXXXXXXXXXXXXXXXIDKPDDVTRDNEKLIILDDDLISTKLISEIEVNEAT 288
            ++LETKIKNVNITQVSSKSSDENMNNSEHIERISDQNA+EDQ+    EV    E  E  VIDKPDDVTRD EKLIILDDDLISTKLISEIEVNEAT
Sbjct:  762 ILLETKIKNVNITQVSSKSSDENMNNSEHIERISDQNAQEDQL--VEEVEVSHESEEFEVIDKPDDVTRDKEKLIILDDDLISTKLISEIEVNEAT 855

HSP 4 Score: 76.6406 bits (187), Expect = 2.928e-170
Identity = 40/40 (100.00%), Postives = 40/40 (100.00%), Query Frame = -2 
Query: 1040 QSPQKSLTRMTSETHKSTKRTPMPPRSRTVERQKPDSIFP 1159
            QSPQKSLTRMTSETHKSTKRTPMPPRSRTVERQKPDSIFP
Sbjct:  482 QSPQKSLTRMTSETHKSTKRTPMPPRSRTVERQKPDSIFP 521
The following BLAST results are available for this feature:
BLAST of SMED30026519 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 SMED30026519 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 SMED30026519 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 SMED30026519 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 SMED30026519 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 SMED30026519 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 SMED30026519 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 SMED30026519 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 SMED30026519 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 SMED30026519 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 SMED30026519 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 SMED30026519 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 SMED30026519 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 SMED30026519 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000064314.12.928e-17098.76SMESG000064314.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026519 ID=SMED30026519|Name=SMED30026519|organism=Schmidtea mediterranea sexual|type=transcript|length=1160bp
CGTTGCTTCATTAACTTCAATTTCAGATATGAGTTTTGTTGAAATTAGAT
CATCATCAAGAATGATCAATTTTTCGTTATCTCTAGTTACATCATCAGGT
TTGTCAATTACAATTACCTCAAATTCTTCGCTTTCGTGGCTAACCTCAAC
CTCTTCGACCATTTGATCCTCTTCAGCATTCTGATCTGATATCCTTTCGA
TATGTTCTGAATTATTCATATTTTCGTCACTTGATTTCGAAGATACTTGG
GTAATATTCACATTCTTGATTTTAGTTTCAAGGATCAAGGAGAATTTCCT
CTGAGTAATCTATAACTTCGAATTGTTCAGCGTCTGGGCTCATCTTTGAT
GAATTACCATTTGAAGTTTCTTGATCCTTGTTTTCTCTTGTGTCATGTGC
TTCCAACGCATCCTTAATGATTTCTAAATTACAAGTTTTTTCCTTATCAC
TATCATCTACATTTTGGATTTCTTTGAGATTATTTGAGATTATAGCTTTA
TTATCTACTTTGTTAAGCGAAATAATTATTTTGCTCATATCCTCATCATT
TTCACTTTTTTTACTAGTTTCTTTAATGTGCTCCTCTATTCCTTTTTCAG
CCGGTTCGAGTGACGCCGAATTACTTTCTTTTATTTCATCTACGGTAATT
TGTTTATTAGTTTCTTGCAGGTTTTGGATTTCAACATTCACGTTGTCATT
TTCAGAATTCTTTTCCAGATCTTTATTTTTTTGAATATCAACTAAATCAA
ATTCTAATGGATTATGGATTTCTTTCTGTAGTTTCCGTTTTATTAACATC
TAAATCAGATACGTATGCGAACTCTTCCACTCCTCCAAGTATTTCCATTG
ACCCAATATTTGTTAAAGTATCTTCATTTGTAATATTATCCGATGATATT
TCTTTACTTTTGCATTCAACAGGTTTAATGTTTTCAGGGACTTCTTTAGT
TACTTTAATCTGTTTTATTTTATTTATTTCTTCAAGACCTATTTTTTTAG
NNNNNNNNNNTTTTTTTTTTTACTTTTAATTAAGGACTTTGGAAAAATAG
AATCTGGTTTCTGTCTTTCAACAGTTCTGGATCTGGGTGGCATTGGGGTT
CTTTTAGTGCTTTTATGAGTTTCAGATGTCATTCTAGTTAGTGATTTTTG
AGGAGATTGT
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protein sequence of SMED30026519-orf-1

>SMED30026519-orf-1 ID=SMED30026519-orf-1|Name=SMED30026519-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=174bp
MLIKRKLQKEIHNPLEFDLVDIQKNKDLEKNSENDNVNVEIQNLQETNKQ
ITVDEIKESNSASLEPAEKGIEEHIKETSKKSENDEDMSKIIISLNKVDN
KAIISNNLKEIQNVDDSDKEKTCNLEIIKDALEAHDTRENKDQETSNGNS
SKMSPDAEQFEVIDYSEEILLDP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000429neoblast
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR018501DDT_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 12..35
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..51