SMED30002697

Overview
NameSMED30002697
Smed IDSMED30002697
Length (bp)1139
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 SMED30002697 (SMED30002697) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002697 (SMED30002697) 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 SMED30002697 (SMED30002697) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002697 (SMED30002697) 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




SMED30002697

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
tail regionSMED30002697SMESG000053884.1 SMESG000053881.1 SmedASXL_079289SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30002697SMESG000053884.1 SMESG000053881.1 dd_Smed_v4_4128_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002697SMESG000053884.1 SMESG000053881.1 dd_Smed_v4_4128_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30002697SMESG000053884.1 SMESG000053881.1 dd_Smed_v4_4128_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30002697SMESG000053884.1 SMESG000053881.1 dd_Smed_v4_4128_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30002697SMESG000053884.1 SMESG000053881.1 dd_Smed_v4_4128_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30002697SMESG000053884.1 SMESG000053881.1 dd_Smed_v6_4128_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
secretory systemSMED30002697SMESG000053884.1 SMESG000053881.1 dd_Smed_v6_4128_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002697 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001130:2297..3479 -5378
v31.000178:149180..150366 +4694
v31.000178:120123..121323 -3536
Homology
BLAST of SMED30002697 vs. Planmine SMEST
Match: SMESG000053884.1 (SMESG000053884.1)

HSP 1 Score: 584.334 bits (1505), Expect = 0.000e+0
Identity = 281/284 (98.94%), Postives = 283/284 (99.65%), Query Frame = 1
Query:   46 FTQSLGSFGCDTSSFEEITTWVGDPTVTVPTETIDECADDCILKSCFGFVYSGGQCTIYHIADHCDQILEQNVIKINVIDTELDKLDILQESFRFNILRNVYAVYNNSYPSIIQSANPSTTQAIINFLNGHTGVMAGTFNNGRALTFYKEECIAIFLALDYVTFSRSLYTNMAKWLTHDACTDFRSCSFHINNYKSYLNKDNQVVLFPQNGISANISDPLLLEKLNSGSWGVIFSGTYWNNILNDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTNANC 897
            FTQSLGSFGCDTSSFEEITTWVGDPTVTVPTETIDECADDCILKSCFGFVY GGQCTIYHIADHCDQILEQNVIKINVIDTELDKLDILQESFRFNILRNVYAVYNNSYPSIIQSANPSTTQAIINFLNGHTGVMAGTFNNGRALTFYKEECIAIFLALDYVTFS+SLYTNMAKWLTHDACTDFRSCSFHINNYKSYLNKDNQVVLFPQNGISANISDPLLLEKLNSGSWGVIFSGTYWNNILNDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTN+NC
Sbjct:    8 FTQSLGSFGCDTSSFEEITTWVGDPTVTVPTETIDECADDCILKSCFGFVYFGGQCTIYHIADHCDQILEQNVIKINVIDTELDKLDILQESFRFNILRNVYAVYNNSYPSIIQSANPSTTQAIINFLNGHTGVMAGTFNNGRALTFYKEECIAIFLALDYVTFSKSLYTNMAKWLTHDACTDFRSCSFHINNYKSYLNKDNQVVLFPQNGISANISDPLLLEKLNSGSWGVIFSGTYWNNILNDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTNSNC 291          
BLAST of SMED30002697 vs. Planmine SMEST
Match: SMESG000053881.1 (SMESG000053881.1)

HSP 1 Score: 584.334 bits (1505), Expect = 0.000e+0
Identity = 281/284 (98.94%), Postives = 283/284 (99.65%), Query Frame = 1
Query:   46 FTQSLGSFGCDTSSFEEITTWVGDPTVTVPTETIDECADDCILKSCFGFVYSGGQCTIYHIADHCDQILEQNVIKINVIDTELDKLDILQESFRFNILRNVYAVYNNSYPSIIQSANPSTTQAIINFLNGHTGVMAGTFNNGRALTFYKEECIAIFLALDYVTFSRSLYTNMAKWLTHDACTDFRSCSFHINNYKSYLNKDNQVVLFPQNGISANISDPLLLEKLNSGSWGVIFSGTYWNNILNDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTNANC 897
            FTQSLGSFGCDTSSFEEITTWVGDPTVTVPTETIDECADDCILKSCFGFVY GGQCTIYHIADHCDQILEQNVIKINVIDTELDKLDILQESFRFNILRNVYAVYNNSYPSIIQSANPSTTQAIINFLNGHTGVMAGTFNNGRALTFYKEECIAIFLALDYVTFS+SLYTNMAKWLTHDACTDFRSCSFHINNYKSYLNKDNQVVLFPQNGISANISDPLLLEKLNSGSWGVIFSGTYWNNILNDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTN+NC
Sbjct:    8 FTQSLGSFGCDTSSFEEITTWVGDPTVTVPTETIDECADDCILKSCFGFVYFGGQCTIYHIADHCDQILEQNVIKINVIDTELDKLDILQESFRFNILRNVYAVYNNSYPSIIQSANPSTTQAIINFLNGHTGVMAGTFNNGRALTFYKEECIAIFLALDYVTFSKSLYTNMAKWLTHDACTDFRSCSFHINNYKSYLNKDNQVVLFPQNGISANISDPLLLEKLNSGSWGVIFSGTYWNNILNDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTNSNC 291          
BLAST of SMED30002697 vs. Planmine SMEST
Match: SMESG000053856.1 (SMESG000053856.1)

HSP 1 Score: 508.834 bits (1309), Expect = 0.000e+0
Identity = 244/279 (87.46%), Postives = 256/279 (91.76%), Query Frame = 1
Query:   61 GSFGCDTSSFEEITTWVGDPTVTVPTETIDECADDCILKSCFGFVYSGGQCTIYHIADHCDQILEQNVIKINVIDTELDKLDILQESFRFNILRNVYAVYNNSYPSIIQSANPSTTQAIINFLNGHTGVMAGTFNNGRALTFYKEECIAIFLALDYVTFSRSLYTNMAKWLTHDACTDFRSCSFHINNYKSYLNKDNQVVLFPQNGISANISDPLLLEKLNSGSWGVIFSGTYWNNILNDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTNANC 897
            GS  C  +SF EITTWVGDP+VT+ T++I ECA  C L   FGFVYS  QCTIYHIADHCDQILEQNVIKINVIDTE  KLDILQ+SFRFNI+RNVYAV NNSYPSIIQSANPS TQAIINFLNGHTGVMAGTFNNGRALTFYK ECI+ FLALDYVTFSRSLYTNMAKWLTHDACTDF SCSFHINNYKSYLNKDNQVVLFPQ+GISANISDPLLLEKLNSGSWG+IFSGTYW++I NDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTNANC
Sbjct:   22 GSLQCQMNSFAEITTWVGDPSVTITTQSIIECAVQCHLLRGFGFVYSNSQCTIYHIADHCDQILEQNVIKINVIDTERQKLDILQKSFRFNIIRNVYAVNNNSYPSIIQSANPSATQAIINFLNGHTGVMAGTFNNGRALTFYKAECISSFLALDYVTFSRSLYTNMAKWLTHDACTDFSSCSFHINNYKSYLNKDNQVVLFPQDGISANISDPLLLEKLNSGSWGIIFSGTYWSSITNDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTNANC 300          
BLAST of SMED30002697 vs. Planmine SMEST
Match: SMESG000053851.1 (SMESG000053851.1)

HSP 1 Score: 480.715 bits (1236), Expect = 1.082e-171
Identity = 231/284 (81.34%), Postives = 247/284 (86.97%), Query Frame = 1
Query:   46 FTQSLGSFGCDTSSFEEITTWVGDPTVTVPTETIDECADDCILKSCFGFVYSGGQCTIYHIADHCDQILEQNVIKINVIDTELDKLDILQESFRFNILRNVYAVYNNSYPSIIQSANPSTTQAIINFLNGHTGVMAGTFNNGRALTFYKEECIAIFLALDYVTFSRSLYTNMAKWLTHDACTDFRSCSFHINNYKSYLNKDNQVVLFPQNGISANISDPLLLEKLNSGSWGVIFSGTYWNNILNDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTNANC 897
            F+QSLGS  C  +SF EITTWVGDP+VT+ T++I ECA  C L   FGFVYS  QCTIYHIADHCDQILEQNVIKINVIDTE  KLDILQ+SFRFNILRNVYAV NNSYPSIIQS NP+ TQAIINFLNGHTGVMAGTFNNGRALTFYKEECI+ FLALDYV +SRSLYTNMAKWLTHDACTDF SCSFHINNYKSYLNKDNQVVL+P   ISAN+SDPLLL K+NSGSWGVIFSGTYW++I NDQRI M KYGICP  S NYGPT+LDLNWCT ISQT N  C
Sbjct:   13 FSQSLGSLECQMNSFAEITTWVGDPSVTITTQSIIECAVQCHLLRGFGFVYSNSQCTIYHIADHCDQILEQNVIKINVIDTERQKLDILQKSFRFNILRNVYAVNNNSYPSIIQSTNPNVTQAIINFLNGHTGVMAGTFNNGRALTFYKEECISSFLALDYVIYSRSLYTNMAKWLTHDACTDFSSCSFHINNYKSYLNKDNQVVLYPSVSISANVSDPLLLAKINSGSWGVIFSGTYWSSITNDQRIWMGKYGICPANSRNYGPTSLDLNWCTGISQTINLKC 296          
BLAST of SMED30002697 vs. Planmine SMEST
Match: SMESG000053851.1 (SMESG000053851.1)

HSP 1 Score: 465.307 bits (1196), Expect = 7.273e-166
Identity = 224/271 (82.66%), Postives = 238/271 (87.82%), Query Frame = 1
Query:   85 SFEEITTWVGDPTVTVPTETIDECADDCILKSCFGFVYSGGQCTIYHIADHCDQILEQNVIKINVIDTELDKLDILQESFRFNILRNVYAVYNNSYPSIIQSANPSTTQAIINFLNGHTGVMAGTFNNGRALTFYKEECIAIFLALDYVTFSRSLYTNMAKWLTHDACTDFRSCSFHINNYKSYLNKDNQVVLFPQNGISANISDPLLLEKLNSGSWGVIFSGTYWNNILNDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTNANC 897
            SF EITTWVGDP+VT+ T++I ECA  C L   FGFVYS  QCTIYHIADHCDQILEQNVIKINVIDTE  KLDILQ+SFRFNILRNVYAV NNSYPSIIQS NP+ TQAIINFLNGHTGVMAGTFNNGRALTFYKEECI+ FLALDYV +SRSLYTNMAKWLTHDACTDF SCSFHINNYKSYLNKDNQVVL+P   ISAN+SDPLLL K+NSGSWGVIFSGTYW++I NDQRI M KYGICP  S NYGPT+LDLNWCT ISQT N  C
Sbjct:    3 SFAEITTWVGDPSVTITTQSIIECAVQCHLLRGFGFVYSNSQCTIYHIADHCDQILEQNVIKINVIDTERQKLDILQKSFRFNILRNVYAVNNNSYPSIIQSTNPNVTQAIINFLNGHTGVMAGTFNNGRALTFYKEECISSFLALDYVIYSRSLYTNMAKWLTHDACTDFSSCSFHINNYKSYLNKDNQVVLYPSVSISANVSDPLLLAKINSGSWGVIFSGTYWSSITNDQRIWMGKYGICPANSRNYGPTSLDLNWCTGISQTINLKC 273          
The following BLAST results are available for this feature:
BLAST of SMED30002697 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 SMED30002697 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 SMED30002697 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 SMED30002697 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 SMED30002697 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 SMED30002697 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 SMED30002697 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 SMED30002697 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 SMED30002697 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 SMED30002697 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 SMED30002697 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 SMED30002697 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 SMED30002697 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 SMED30002697 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000053884.10.000e+098.94SMESG000053884.1[more]
SMESG000053881.10.000e+098.94SMESG000053881.1[more]
SMESG000053856.10.000e+087.46SMESG000053856.1[more]
SMESG000053851.11.082e-17181.34SMESG000053851.1[more]
SMESG000053851.17.273e-16682.66SMESG000053851.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002697 ID=SMED30002697|Name=SMED30002697|organism=Schmidtea mediterranea sexual|type=transcript|length=1139bp
GTTTTCCTGTAGGAAATCATTATCATGTTGCTGGTATTAATACTATTCAC
TCAAAGCCTTGGCTCATTTGGATGTGATACGAGCTCATTTGAAGAAATAA
CAACCTGGGTTGGAGACCCCACCGTCACCGTGCCCACTGAAACCATCGAT
GAATGTGCTGACGATTGCATATTAAAAAGTTGTTTTGGATTCGTCTATTC
CGGCGGCCAGTGTACGATTTATCATATTGCTGATCATTGCGATCAAATCC
TTGAACAGAATGTTATCAAAATTAATGTCATCGATACTGAACTGGATAAG
TTGGATATTTTACAAGAATCATTCCGTTTCAATATTCTCCGGAACGTTTA
CGCAGTTTATAACAATTCTTATCCGTCAATTATACAATCCGCCAATCCAA
GTACAACGCAAGCCATAATTAATTTCCTTAATGGTCACACTGGTGTTATG
GCGGGTACATTTAATAATGGTCGGGCATTGACATTTTACAAGGAAGAATG
TATTGCCATATTCCTTGCACTTGACTATGTAACTTTTAGCCGAAGTTTAT
ATACAAATATGGCAAAATGGCTGACTCATGACGCGTGTACAGATTTCCGC
AGTTGCTCGTTCCACATCAACAATTATAAATCGTATTTGAATAAAGATAA
TCAAGTTGTCCTTTTTCCTCAAAACGGTATCAGCGCGAATATCAGCGATC
CGCTTTTACTCGAAAAACTAAATTCCGGAAGTTGGGGAGTAATTTTTTCT
GGCACTTATTGGAATAATATTTTAAATGACCAACGGATATTGATGAAAAA
GTATGGTATATGTCCGACAGGTTCAATGAATTATGGACCGACTGCTTTGG
ACCTAAACTGGTGCACAAAAATTTCCCAAACAACAAATGCAAACTGTTGA
AGAATTGTTATAGTTCTATATAACTGAATATGCAAAATAAATTGTTTTGA
ATTTGAATTTGTGTTTTAATAAATCTATTTTTATCTTTCACCAGTAGGAT
AATATGAGCTCCTTCCGTATACAATGAGGACAATTATCTTTCTAATATTT
GGCTTGAGGTTTCTGGTGTCTTCTCTTCTTAAAAAATAGGCCGGTTGTTA
AAAACGTTTTTAAAATAATTTTTGTTTAAATGAAGTGAG
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protein sequence of SMED30002697-orf-1

>SMED30002697-orf-1 ID=SMED30002697-orf-1|Name=SMED30002697-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=292bp
MLLVLILFTQSLGSFGCDTSSFEEITTWVGDPTVTVPTETIDECADDCIL
KSCFGFVYSGGQCTIYHIADHCDQILEQNVIKINVIDTELDKLDILQESF
RFNILRNVYAVYNNSYPSIIQSANPSTTQAIINFLNGHTGVMAGTFNNGR
ALTFYKEECIAIFLALDYVTFSRSLYTNMAKWLTHDACTDFRSCSFHINN
YKSYLNKDNQVVLFPQNGISANISDPLLLEKLNSGSWGVIFSGTYWNNIL
NDQRILMKKYGICPTGSMNYGPTALDLNWCTKISQTTNANC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000421tail
PLANA:0000484secretory system
PLANA:0003117parapharyngeal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..16
score: 0.733