SMED30004106

Overview
NameSMED30004106
Smed IDSMED30004106
Length (bp)567
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 SMED30004106 (SMED30004106) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004106 (SMED30004106) 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.
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




SMED30004106

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
intestinal phagocyteSMED30004106SMESG000069968.1 Contig3166newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30004106 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003462:45579..46178 +2690
v31.007931:8787..9385 +2609
v31.011374:14747..15345 +2573
v31.005715:17127..17733 +2551
v31.001606:44781..45379 -2537
v31.001433:53463..54063 -2522
v31.000082:12459..13060 -2513
v31.010265:9666..10272 +2479
v31.003801:41022..41616 -2418
v31.025150:3028..3618 +2368
v31.003115:36767..37361 -2295
v31.000594:81980..82573 +2273
v31.019671:4110..4718 +2262
v31.002944:11184..11792 +2253
v31.004582:40750..41344 -2213
v31.017722:8064..8661 +2197
v31.000708:67907..68501 +2195
v31.000645:74082..74676 -2195
v31.000645:45229..45823 -2195
v31.003043:5769..6365 +2179
v31.026007:9739..10337 -2170
v31.003907:868..1462 +2169
v31.002943:51915..52511 +2169
v31.002659:25857..26451 +2168
v31.003354:35053..35646 +2125
v31.001314:78063..78655 -2117
v31.000218:12806..13399 +2116
v31.000002:501598..502191 -2107
v31.000652:39286..39959 -2101
v31.001135:46588..47265 -2095
v31.003510:34887..35548 +2089
v31.001143:60767..61354 +2084
v31.003645:63662..64258 +2071
v31.001848:7468..8058 -2070
v31.023612:3981..4643 +2069
v31.026470:7173..7835 -2068
v31.000255:86919..87581 -2068
v31.004827:17854..18450 +2064
v31.000968:31343..32005 -2061
v31.001964:9303..9965 -2059
v31.000182:187354..187951 +2055
v31.000006:295778..296374 -2055
v31.002697:32362..32952 +2054
v31.012485:14241..14894 +2051
v31.000638:96789..97451 +2048
v31.002773:79767..80403 +2044
v31.001814:86715..87376 +2043
v31.003339:3367..4029 -2042
v31.000366:152412..153073 +2039
v31.011271:11113..11774 +2037
v31.009396:8694..9355 -2035
v31.001379:30157..30818 -2035
v31.004898:17802..18399 +2028
v31.002670:48799..49458 +2028
v31.022742:3038..3698 +2027
v31.000174:190067..190723 +2022
v31.017488:8541..9201 +2018
v31.013484:8112..8773 +2016
v31.004315:28188..28848 -2009
v31.000032:215327..215915 -2009
v31.001906:51457..52118 +2007
v31.013849:6923..7584 +2005
v31.004035:35445..36033 -2004
v31.002977:8516..9176 +2000
v31.034580:576..1237 -1999
v31.006287:13284..13941 +1997
v31.020160:4563..5225 +1996
v31.016902:6146..6731 +1992
v31.026781:1385..2045 +1991
v31.001299:59804..60465 -1990
v31.000372:115733..116409 +1988
v31.002393:24040..24636 +1984
v31.002039:10372..10966 -1979
v31.001346:52913..53573 -1963
v31.014953:4752..5414 +1960
v31.013381:7978..8639 +1954
v31.001048:63194..64890 +1941
v31.006398:2941..3530 +1935
v31.002246:46357..46946 +1935
v31.000009:293629..294218 -1935
v31.004940:11020..11610 +1934
v31.019738:5126..5718 -1933
v31.001798:40507..41167 -1933
v31.002622:35978..36568 -1931
v31.006880:14678..15268 -1928
v31.019023:2834..3470 -1926
v31.002907:41303..41893 -1926
v31.015633:645..1233 +1924
v31.019619:3629..4216 -1923
v31.006996:8862..9452 -1923
v31.000184:55161..55823 -1923
v31.019312:4722..5256 +1917
v31.009971:9277..9866 +1908
v31.000666:150368..150962 -1906
v31.003551:17884..18474 -1905
v31.007743:10463..11052 -1904
v31.037783:1209..1796 -1893
v31.000528:65491..66080 -1893
v31.003024:2652..3239 -1891
v31.002421:68016..68603 +1891
v31.000141:64625..65217 +1884
v31.003218:43366..43954 -1878
v31.002393:33933..34489 +1877
v31.000923:112084..112734 +1873
v31.000210:54955..55542 -1873
v31.021057:7487..8064 +1870
v31.001084:50900..51489 +1865
v31.007124:6557..7148 -1857
v31.001718:45025..45618 -1856
v31.006575:20383..20970 -1855
v31.001048:63212..63781 +1838
v31.014231:11900..12480 +1828
v31.005794:16515..17097 -1817
v31.009603:15128..15706 -1814
v31.000902:18748..19322 +1812
v31.013407:18271..18857 -1805
v31.000018:58609..59185 +1788
v31.001235:43172..43778 -1763
v31.008916:6266..6911 +1760
v31.006924:23176..23783 +1661
Homology
BLAST of SMED30004106 vs. Planmine SMEST
Match: SMESG000033377.1 (SMESG000033377.1)

HSP 1 Score: 96.6709 bits (239), Expect = 2.209e-23
Identity = 44/51 (86.27%), Postives = 47/51 (92.16%), Query Frame = -3
Query:   80 LITPILSIFQAFMLWKPLGLNKYYRENDLVLSHRDLSYSYQCRLNLIMLQG 232
            +ITPILSIF+AFMLWK LGLN+YYRENDLVLSHRDLSYSYQCRLN I LQ 
Sbjct:   33 IITPILSIFKAFMLWKSLGLNRYYRENDLVLSHRDLSYSYQCRLNSIRLQA 83          

HSP 2 Score: 58.5362 bits (140), Expect = 3.290e-10
Identity = 28/52 (53.85%), Postives = 35/52 (67.31%), Query Frame = -2
Query:  168 CVITPLYRNFNFIDMLVVRLLAPLDFTNA*PYHSDIINFSGFHVMEAVGFKQ 323
            C IT  YRNFNF+DMLVVRLLAPLDFTNA      +  F  F + +++G  +
Sbjct:    3 CFITSFYRNFNFVDMLVVRLLAPLDFTNAYIITPILSIFKAFMLWKSLGLNR 54          
The following BLAST results are available for this feature:
BLAST of SMED30004106 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 SMED30004106 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 SMED30004106 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 SMED30004106 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 SMED30004106 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 SMED30004106 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 SMED30004106 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 SMED30004106 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 SMED30004106 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 SMED30004106 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 SMED30004106 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 SMED30004106 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 SMED30004106 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 SMED30004106 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000033377.12.209e-2386.27SMESG000033377.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004106 ID=SMED30004106|Name=SMED30004106|organism=Schmidtea mediterranea sexual|type=transcript|length=567bp
TCGCATTTTTTTTTTTTTTTTTTAACAAAAAATTGAATAACAGTTTATTG
ACATAAAATTACTGTTAAGGAGTTACACAACCTTGCAGCATTATTAAATT
CAATCGACATTGATAGGAATAGCTTAAATCACGGTGAGAAAGAACCAAAT
CATTTTCACGATAATATTTGTTTAAACCCAACGGCTTCCATAACATGAAA
GCCTGAAAAATTGATAATATCGGAGTGATAAGGTTAAGCATTAGTAAAAT
CCAATGGCGCTAATAGACGAACCACCAACATGTCGATAAAGTTAAAATTC
CGATAGAGTGGAGTAATAACACATCCCAAAAAGTTAGAACAGGAATCGAG
CAAATGCAACCAAAATTCCAACTCGTTCAAATGATTAAAAATGTCGTGAT
CTAATAGTATATCTAATCAACCAAACAGCGAAAATACGCCGGATATTGAA
TTATACCGGAAATCGCACCAATCTACCCGAACATCCTTGAACAACACTAG
TAAAATAACATCCGGACTAAATGTCCACTAAATCTAAAGTCATCAATCAC
GTTTCTATCTGACCGGA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte