SMED30023908

Overview
NameSMED30023908
Smed IDSMED30023908
Length (bp)416
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 SMED30023908 (SMED30023908) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023908 (SMED30023908) 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 SMED30023908 (SMED30023908) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023908 (SMED30023908) 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.
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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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Alignments
SMED30023908 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000164:137987..138402 +2035
v31.006223:2997..3448 -2023
v31.020771:2511..2926 -2008
v31.003181:45828..46244 -2005
v31.040513:2497..2912 +1990
v31.002520:65880..66295 -1990
v31.003693:65502..65918 -1987
v31.005384:98..513 +1981
v31.037312:1194..1627 -1974
v31.037570:1207..1622 -1972
v31.001245:526..941 -1972
v31.000234:99347..99762 -1972
v31.001227:77699..78114 +1963
v31.000816:96414..96829 -1963
v31.038971:1457..1872 -1954
v31.000559:22829..23244 -1954
v31.024943:1282..1697 -1945
v31.016334:2067..2482 -1945
v31.027024:8521..8935 +1940
v31.004799:26176..26590 +1937
v31.013918:10273..10688 -1936
v31.046612:3624..4040 -1933
v31.041560:4228..4642 -1874
v31.005384:10594..11009 +1873
v31.002338:14360..14774 +1829
v31.017042:5693..6105 -1813
v31.013645:12004..12407 -1813
v31.007800:8303..8700 +1796
v31.003364:63722..64144 -1784
v31.025202:1220..1638 +1782
v31.018981:4560..5137 +1776
v31.018697:1970..2391 +1770
v31.018530:8316..8746 +1743
v31.004485:44878..45308 +1743
v31.021238:6034..6437 -1696
v31.015796:1871..2268 +1579
v31.010292:23341..23721 +1412
v31.013705:5181..5585 +1368
v31.015411:4022..4454 +1121
v31.001780:50853..51255 +1022
v31.000422:42848..43378 -758
v31.010292:23262..23737 +673
v31.022329:8418..8986 +649
v31.005384:10462..10849 -527
v31.018530:8154..8563 -512
v31.013705:5019..5548 +507
v31.015796:1757..2168 +499
v31.015796:1715..2125 +477
v31.018530:8208..8614 -463
v31.021238:6186..6575 -462
v31.005384:10444..10818 -455
v31.010157:13205..13606 +443
v31.030663:122..464 +437
v31.000013:380265..380670 +424
Homology
BLAST of SMED30023908 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1)

HSP 1 Score: 197.208 bits (500), Expect = 3.916e-59
Identity = 97/104 (93.27%), Postives = 100/104 (96.15%), Query Frame = 2
Query:  104 QVGGSLEPIIQINLNGAIKTIKFNTSEAQLIKIMLTERISSKLFDEIGKMGGDVKIQFAVLIQFEKDGEIRDNYFSNNAEKFSDSFLSEGVNKLNEKIEKFTHL 415
            QVGGSL+PIIQINLNGAIKTIKF+TSEA+LIKIMLTERISSKL DEIGKMG DVKIQFAVL QFEKDGEIRDNYFSNNAEKFSDSF SEGVNKLNEKIEKFTHL
Sbjct:  897 QVGGSLKPIIQINLNGAIKTIKFDTSEARLIKIMLTERISSKLIDEIGKMGADVKIQFAVLTQFEKDGEIRDNYFSNNAEKFSDSFFSEGVNKLNEKIEKFTHL 1000          
BLAST of SMED30023908 vs. Planmine SMEST
Match: SMESG000058180.1 (SMESG000058180.1)

HSP 1 Score: 195.667 bits (496), Expect = 7.275e-59
Identity = 98/104 (94.23%), Postives = 100/104 (96.15%), Query Frame = 2
Query:  104 QVGGSLEPIIQINLNGAIKTIKFNTSEAQLIKIMLTERISSKLFDEIGKMGGDVKIQFAVLIQFEKDGEIRDNYFSNNAEKFSDSFLSEGVNKLNEKIEKFTHL 415
            QVGGSLEPIIQINLNGAIKTIKFNTS+ +LIKIMLTERISSKL DEIGKM GDVKIQFAVLIQFEKDGEIRDNYFSNNAEK SDSFLSEGVNKLNEKIEKFTHL
Sbjct:  556 QVGGSLEPIIQINLNGAIKTIKFNTSDVRLIKIMLTERISSKLIDEIGKMEGDVKIQFAVLIQFEKDGEIRDNYFSNNAEKCSDSFLSEGVNKLNEKIEKFTHL 659          
BLAST of SMED30023908 vs. Planmine SMEST
Match: SMESG000058180.1 (SMESG000058180.1)

HSP 1 Score: 195.667 bits (496), Expect = 8.602e-59
Identity = 98/104 (94.23%), Postives = 100/104 (96.15%), Query Frame = 2
Query:  104 QVGGSLEPIIQINLNGAIKTIKFNTSEAQLIKIMLTERISSKLFDEIGKMGGDVKIQFAVLIQFEKDGEIRDNYFSNNAEKFSDSFLSEGVNKLNEKIEKFTHL 415
            QVGGSLEPIIQINLNGAIKTIKFNTS+ +LIKIMLTERISSKL DEIGKM GDVKIQFAVLIQFEKDGEIRDNYFSNNAEK SDSFLSEGVNKLNEKIEKFTHL
Sbjct:  565 QVGGSLEPIIQINLNGAIKTIKFNTSDVRLIKIMLTERISSKLIDEIGKMEGDVKIQFAVLIQFEKDGEIRDNYFSNNAEKCSDSFLSEGVNKLNEKIEKFTHL 668          
BLAST of SMED30023908 vs. Planmine SMEST
Match: SMESG000048922.1 (SMESG000048922.1)

HSP 1 Score: 153.295 bits (386), Expect = 8.684e-44
Identity = 79/107 (73.83%), Postives = 91/107 (85.05%), Query Frame = 2
Query:  104 QVGGSL---EPIIQINLNGAIKTIKFNTSEAQLIKIMLTERISSKLFDEIGKMGGDVKIQFAVLIQFEKDGEIRDNYFSNNAEKFSDSFLSEGVNKLNEKIEKFTHL 415
            Q GGS+   EP I +NLNGAIKT++F+ S A+LI + LTERIS+KL  EI KMG  VKIQFA+LI+FEKDGEIRDNYFSNNAE FSD+FLSEGVNKLNEKIE+FTHL
Sbjct: 1106 QFGGSVLENEPNISVNLNGAIKTLRFDISNAELITVTLTERISNKLIFEINKMGS-VKIQFAILIKFEKDGEIRDNYFSNNAETFSDNFLSEGVNKLNEKIEQFTHL 1211          
BLAST of SMED30023908 vs. Planmine SMEST
Match: SMESG000048922.1 (SMESG000048922.1)

HSP 1 Score: 152.91 bits (385), Expect = 1.086e-43
Identity = 79/107 (73.83%), Postives = 91/107 (85.05%), Query Frame = 2
Query:  104 QVGGSL---EPIIQINLNGAIKTIKFNTSEAQLIKIMLTERISSKLFDEIGKMGGDVKIQFAVLIQFEKDGEIRDNYFSNNAEKFSDSFLSEGVNKLNEKIEKFTHL 415
            Q GGS+   EP I +NLNGAIKT++F+ S A+LI + LTERIS+KL  EI KMG  VKIQFA+LI+FEKDGEIRDNYFSNNAE FSD+FLSEGVNKLNEKIE+FTHL
Sbjct: 1148 QFGGSVLENEPNISVNLNGAIKTLRFDISNAELITVTLTERISNKLIFEINKMGS-VKIQFAILIKFEKDGEIRDNYFSNNAETFSDNFLSEGVNKLNEKIEQFTHL 1253          
The following BLAST results are available for this feature:
BLAST of SMED30023908 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 SMED30023908 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 SMED30023908 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 SMED30023908 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 SMED30023908 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 SMED30023908 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 SMED30023908 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 SMED30023908 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 SMED30023908 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 SMED30023908 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 SMED30023908 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 SMED30023908 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 SMED30023908 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 SMED30023908 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000057533.13.916e-5993.27SMESG000057533.1[more]
SMESG000058180.17.275e-5994.23SMESG000058180.1[more]
SMESG000058180.18.602e-5994.23SMESG000058180.1[more]
SMESG000048922.18.684e-4473.83SMESG000048922.1[more]
SMESG000048922.11.086e-4373.83SMESG000048922.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023908 ID=SMED30023908|Name=SMED30023908|organism=Schmidtea mediterranea sexual|type=transcript|length=416bp
TAATGCAGATATTGTAAATAATGCAGATATTATAAATATTGCAGACATTG
TAAATAATGTAGATATTATAAATAATGTAGATATTGTTAATAATACTATT
AATCAAGTTGGTGGTTCATTAGAACCTATAATACAAATTAATTTAAACGG
CGCAATTAAAACAATTAAATTTAATACATCAGAGGCGCAACTGATAAAAA
TAATGTTAACTGAGAGAATCAGTTCTAAATTATTTGATGAGATTGGAAAG
ATGGGGGGTGATGTTAAAATTCAATTTGCTGTTTTAATACAGTTTGAAAA
AGATGGGGAAATCCGCGATAATTATTTTTCCAACAACGCAGAAAAATTTT
CAGATAGTTTTTTATCTGAAGGAGTTAATAAACTCAATGAAAAAATAGAA
AAGTTCACCCATTTAG
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protein sequence of SMED30023908-orf-1

>SMED30023908-orf-1 ID=SMED30023908-orf-1|Name=SMED30023908-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=138bp
NADIVNNADIINIADIVNNVDIINNVDIVNNTINQVGGSLEPIIQINLNG
AIKTIKFNTSEAQLIKIMLTERISSKLFDEIGKMGGDVKIQFAVLIQFEK
DGEIRDNYFSNNAEKFSDSFLSEGVNKLNEKIEKFTHL
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland