Si:ch211-258f14.2

Overview
NameSi:ch211-258f14.2
Smed IDSMED30014024
Length (bp)1768
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 Si:ch211-258f14.2 (SMED30014024) t-SNE clustered cells

Violin plots show distribution of expression levels for Si:ch211-258f14.2 (SMED30014024) 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 Si:ch211-258f14.2 (SMED30014024) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Si:ch211-258f14.2 (SMED30014024) 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




SMED30014024

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30014024h1SMcG0001533 SmedASXL_015405SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
cephalic gangliaSMED30014024h1SMcG0001533 dd_Smed_v4_16356_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30014024h1SMcG0001533 dd_Smed_v4_16356_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30014024h1SMcG0001533 dd_Smed_v6_16356_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Si:ch211-258f14.2 vs. Planmine SMEST
Match: SMESG000032040.1 (SMESG000032040.1)

HSP 1 Score: 999.964 bits (2584), Expect = 0.000e+0
Identity = 539/542 (99.45%), Postives = 540/542 (99.63%), Query Frame = 1
Query:   70 MTSGVGTKSIPKDYRFENILRMNLTADKFDKIIYYDTCIILKPNKVYGKXXXXXXXXXXXXXXXKTFSVLADFKDIVKIELLNDIPQFIVGPMRNDCIHVKILYKIKSKEVKIQIKDKSTNNMALCCNHCTKELDTSNQLLLATENLSEEMTSNTQDNNYHDNAININEGPMDSIHFYILNKFSPVMTLLKKSYVDYLIRETLQYSPIYNLPSSHLTQSLINNLFDGLXXXXXXXXXXXGTSRDFLVELMQSGYKYTRIRILFWSKSNLFESLVEQSTEELKVLMSLDQLGNCSESVSNTPTKQLIVSSXXXXXXXXXXXXXXXXETDHLHSKWEQLRKNNGKFSLLLTENLMILVAYLNRHDRYDEISHEKSSEFDVDIDYVKHEITVNSIQLFYNLICSAQVTFNNAAEINTFTTRNISNLIESLTSYDDNQAVFNSFINQIMHMVFVWLFPKVYKLTNQTELSPQQVVSMFQLFTSLKILVNCLPKIIDIFRREMKEEFHYFVLQEITFCGTYPLSKPTVELLKTFQKNMTNLNQIFVN 1695
            MTSGVGTKSIPKDYRFENILRMNLTADKFDKIIYYDTCIILKPNKVYGKIIISDDCIYSYIEISKTFSVLADFKDIVKIELLNDIPQFIVGPMRNDCIHVKILYKIKSKEVKIQIKDKSTNNMALCCNHCTKELDTSNQLLLATENLSEEMTSNTQDNNYHDNAININEGPMDSI FYILNKFSPVMTLLKKSYVDYLIRETLQYSPIYNLPSSHLTQSLINNLFDGLIIDISKSIKSIGTSRDFLVELMQSGYKYTRIRILFWSKSNLFESLVEQSTEELKVLMSLDQLGNCSESVSNTPTKQLIVSSLNSINLFLKIFNIFFFETDHLHSKWEQLRKNNGKFSL+LTENLMILVAYLNRHDRYDEISHEKSSEFDVDIDYVKHEITVNSIQLFYNLICSAQVTFNNAAEINTFTTRNISNLIESLTSYDDNQAVFNSFINQIMHMVFVWLFPKVYKLTNQTELSPQQVVSMFQLFTSLKILVNCLPKIIDIFRREMKEEFHYF LQEITFCGTYPLSKPTVELLKTFQKNMTNLNQIFVN
Sbjct:    1 MTSGVGTKSIPKDYRFENILRMNLTADKFDKIIYYDTCIILKPNKVYGKIIISDDCIYSYIEISKTFSVLADFKDIVKIELLNDIPQFIVGPMRNDCIHVKILYKIKSKEVKIQIKDKSTNNMALCCNHCTKELDTSNQLLLATENLSEEMTSNTQDNNYHDNAININEGPMDSIDFYILNKFSPVMTLLKKSYVDYLIRETLQYSPIYNLPSSHLTQSLINNLFDGLIIDISKSIKSIGTSRDFLVELMQSGYKYTRIRILFWSKSNLFESLVEQSTEELKVLMSLDQLGNCSESVSNTPTKQLIVSSLNSINLFLKIFNIFFFETDHLHSKWEQLRKNNGKFSLILTENLMILVAYLNRHDRYDEISHEKSSEFDVDIDYVKHEITVNSIQLFYNLICSAQVTFNNAAEINTFTTRNISNLIESLTSYDDNQAVFNSFINQIMHMVFVWLFPKVYKLTNQTELSPQQVVSMFQLFTSLKILVNCLPKIIDIFRREMKEEFHYFSLQEITFCGTYPLSKPTVELLKTFQKNMTNLNQIFVN 542          
The following BLAST results are available for this feature:
BLAST of Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 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 Si:ch211-258f14.2 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000032040.10.000e+099.45SMESG000032040.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014024 ID=SMED30014024|Name=Si:ch211-258f14.2|organism=Schmidtea mediterranea sexual|type=transcript|length=1768bp
ATTTGATTTCAAATTCATTAACTAATATCATTTATTAAAGTAATTGTGAA
TTAAGATTATTTACTCATTATGACTAGTGGTGTCGGAACGAAAAGTATTC
CAAAAGATTATCGGTTTGAAAATATTTTAAGAATGAATTTGACGGCGGAT
AAATTCGATAAAATTATATATTATGATACATGCATCATACTGAAACCTAA
TAAAGTGTATGGAAAAATAATAATTAGCGACGATTGTATTTATTCGTACA
TAGAGATTAGCAAAACATTTTCTGTCTTAGCTGATTTTAAAGATATCGTA
AAAATCGAATTACTCAATGATATCCCCCAATTTATAGTGGGACCCATGAG
AAATGATTGTATTCACGTGAAGATACTCTACAAAATAAAATCAAAAGAAG
TGAAAATTCAAATTAAAGACAAATCAACCAATAACATGGCGCTGTGTTGT
AATCATTGCACAAAAGAACTAGATACCTCAAATCAATTGCTATTAGCAAC
TGAAAATCTAAGCGAGGAAATGACCTCTAATACCCAGGACAATAATTACC
ATGACAATGCAATAAATATTAATGAGGGGCCAATGGATTCTATTCATTTT
TACATTTTGAATAAATTCTCTCCTGTAATGACATTGTTAAAAAAGTCGTA
TGTTGATTATTTAATCCGTGAAACTTTGCAATATTCTCCAATTTATAATC
TACCCAGTTCTCATCTAACGCAGTCTCTGATAAATAATTTGTTTGACGGG
CTGATTATTGACATTTCCAAATCTATCAAATCAATCGGTACTAGTAGAGA
TTTTCTGGTAGAATTAATGCAATCAGGTTACAAATACACTCGGATTAGAA
TTTTATTTTGGTCGAAATCGAATTTATTTGAATCTCTAGTCGAACAATCC
ACTGAGGAATTGAAGGTTTTGATGTCGCTTGATCAATTAGGCAATTGCTC
AGAGTCAGTTTCAAATACACCGACGAAACAGTTGATCGTTTCTTCATTAA
ACTCCATTAATTTATTTTTGAAAATTTTCAACATATTTTTCTTCGAAACC
GATCATCTCCATTCGAAATGGGAACAATTGCGAAAGAATAATGGAAAGTT
TTCGTTGCTATTAACAGAAAATCTCATGATTTTGGTGGCTTATTTAAACC
GCCATGATCGATATGACGAAATTTCTCATGAGAAATCTTCTGAATTTGAT
GTCGATATTGACTATGTTAAACATGAAATTACTGTCAATTCGATTCAACT
GTTTTACAATCTGATCTGTTCGGCTCAAGTCACATTCAATAATGCCGCGG
AAATCAACACATTCACCACTCGAAATATTAGCAATTTGATTGAATCTCTC
ACTTCCTATGATGACAATCAAGCGGTATTCAATTCATTTATCAATCAAAT
TATGCACATGGTGTTTGTTTGGCTTTTTCCGAAAGTCTACAAACTGACCA
ATCAAACCGAATTGTCGCCGCAACAAGTCGTTTCAATGTTCCAATTGTTC
ACATCACTAAAAATATTAGTCAATTGTTTACCGAAAATTATCGACATTTT
TCGACGAGAAATGAAAGAAGAATTTCATTATTTTGTCTTGCAGGAAATAA
CTTTCTGTGGCACTTATCCATTGTCAAAACCGACTGTGGAATTGTTGAAA
ACATTCCAAAAGAACATGACAAATTTGAATCAGATATTTGTCAACTGACT
GCGGATTTAAGTGACTTTAATTAATAGATGCAATTTTGTTTCAACTTCAA
TTTGTAATTTTTAGAGCC
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protein sequence of SMED30014024-orf-1

>SMED30014024-orf-1 ID=SMED30014024-orf-1|Name=SMED30014024-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=543bp
MTSGVGTKSIPKDYRFENILRMNLTADKFDKIIYYDTCIILKPNKVYGKI
IISDDCIYSYIEISKTFSVLADFKDIVKIELLNDIPQFIVGPMRNDCIHV
KILYKIKSKEVKIQIKDKSTNNMALCCNHCTKELDTSNQLLLATENLSEE
MTSNTQDNNYHDNAININEGPMDSIHFYILNKFSPVMTLLKKSYVDYLIR
ETLQYSPIYNLPSSHLTQSLINNLFDGLIIDISKSIKSIGTSRDFLVELM
QSGYKYTRIRILFWSKSNLFESLVEQSTEELKVLMSLDQLGNCSESVSNT
PTKQLIVSSLNSINLFLKIFNIFFFETDHLHSKWEQLRKNNGKFSLLLTE
NLMILVAYLNRHDRYDEISHEKSSEFDVDIDYVKHEITVNSIQLFYNLIC
SAQVTFNNAAEINTFTTRNISNLIESLTSYDDNQAVFNSFINQIMHMVFV
WLFPKVYKLTNQTELSPQQVVSMFQLFTSLKILVNCLPKIIDIFRREMKE
EFHYFVLQEITFCGTYPLSKPTVELLKTFQKNMTNLNQIFVN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR027878DUF4551
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR027878Protein of unknown function DUF4551PFAMPF15087DUF4551coord: 146..528
e-value: 1.2E-17
score: 64.0
coord: 13..136
e-value: 3.1E-18
score: 66.0
IPR027878Protein of unknown function DUF4551PANTHERPTHR35354FAMILY NOT NAMEDcoord: 10..131
coord: 146..532