Neoblast Clusters
Zeng et. al., 2018
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 SMED30025868 (SMED30025868) t-SNE clustered cells
Violin plots show distribution of expression levels for SMED30025868 (SMED30025868) 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 SMED30025868 (SMED30025868) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.
Violin plots show distribution of expression levels for SMED30025868 (SMED30025868) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.
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Homology
BLAST of SMED30025868 vs. Planmine SMEST
Match:
SMESG000076760.1 (SMESG000076760.1)
HSP 1 Score: 466.077 bits (1198), Expect = 2.055e-157
Identity = 239/261 (91.57%), Postives = 252/261 (96.55%), Query Frame = 2
Query: 1238 MNNENSEKYCDYYQRPGHRSSKYHAQIECWNCGKLGHTATRCRVPKISFQCWQENHLPAAYRTRRNHDQNNNTKTPESKSTEMKNEINMPARMCNYLAVDQPHTKINQQSEINVLQGTSRKQQIKCDPIKHQQDWNTLKITEGLEAEKRYSEIGTFQAXXXXXXXXXXXXXXXXADIIKLTTNDSQVEKINEMWEKRINGVLRINMMRAITKKEPSVQRIPQIKIESEIIERMENVNLNNEDHNEPAMGSDVNRNIETRNQ 2020
M++ENSEKYCDYYQR HRSSKYHAQIECWNCGKLGHTATRCR+PKISFQC QENHLPAAYRTRRNHD+NNNTKTPESK TEM+NE +MPARMC+YLAVDQPHT+INQQSEINVLQG SRKQQIKCDPIKHQQDWNTLKITE LEAEKRYSE+GTFQARIEEER RRRKEELLKADIIKLTTNDSQV+KINEMWEKRI+GVLRINMMRAITKKEPSVQ+IPQI+IESEIIERMENVNLNNEDHNEPAMGSDVNRNIETR Q
Sbjct: 1 MSSENSEKYCDYYQRSCHRSSKYHAQIECWNCGKLGHTATRCRLPKISFQCRQENHLPAAYRTRRNHDENNNTKTPESKLTEMQNEKDMPARMCSYLAVDQPHTEINQQSEINVLQGISRKQQIKCDPIKHQQDWNTLKITEALEAEKRYSEMGTFQARIEEERWRRRKEELLKADIIKLTTNDSQVKKINEMWEKRIHGVLRINMMRAITKKEPSVQKIPQIRIESEIIERMENVNLNNEDHNEPAMGSDVNRNIETRTQ 261
BLAST of SMED30025868 vs. Planmine SMEST
Match:
SMESG000000690.1 (SMESG000000690.1)
HSP 1 Score: 464.151 bits (1193), Expect = 2.678e-154
Identity = 237/261 (90.80%), Postives = 250/261 (95.79%), Query Frame = 2
Query: 1238 MNNENSEKYCDYYQRPGHRSSKYHAQIECWNCGKLGHTATRCRVPKISFQCWQENHLPAAYRTRRNHDQNNNTKTPESKSTEMKNEINMPARMCNYLAVDQPHTKINQQSEINVLQGTSRKQQIKCDPIKHQQDWNTLKITEGLEAEKRYSEIGTFQAXXXXXXXXXXXXXXXXADIIKLTTNDSQVEKINEMWEKRINGVLRINMMRAITKKEPSVQRIPQIKIESEIIERMENVNLNNEDHNEPAMGSDVNRNIETRNQ 2020
MNNENSEKYCD+YQRPGHRSSKYHAQIECWNCGK GHTATRCR+PKISFQCWQENHLPAAYRTRRNHD+NNNTKTPESKSTE++NEIN+P RMC+Y A +QPHT+INQQSE NVLQG SRKQQIK DPIKHQQDWNTLK+TE LEAEKRYSEI TFQARIEEER RRRKEELLKADIIKLTTNDSQV+KINEMWEKRINGV RINMMRAITKKEPSVQRIPQI+IESEIIERMENVNLNNEDHNEPA+GSDVNRNIETRNQ
Sbjct: 1 MNNENSEKYCDHYQRPGHRSSKYHAQIECWNCGKSGHTATRCRIPKISFQCWQENHLPAAYRTRRNHDENNNTKTPESKSTELQNEINIPTRMCSYFADNQPHTEINQQSEKNVLQGISRKQQIKWDPIKHQQDWNTLKMTEALEAEKRYSEIRTFQARIEEERWRRRKEELLKADIIKLTTNDSQVKKINEMWEKRINGVQRINMMRAITKKEPSVQRIPQIRIESEIIERMENVNLNNEDHNEPAVGSDVNRNIETRNQ 261
BLAST of SMED30025868 vs. Planmine SMEST
Match:
SMESG000028769.1 (SMESG000028769.1)
HSP 1 Score: 459.914 bits (1182), Expect = 1.333e-153
Identity = 233/261 (89.27%), Postives = 247/261 (94.64%), Query Frame = 2
Query: 1238 MNNENSEKYCDYYQRPGHRSSKYHAQIECWNCGKLGHTATRCRVPKISFQCWQENHLPAAYRTRRNHDQNNNTKTPESKSTEMKNEINMPARMCNYLAVDQPHTKINQQSEINVLQGTSRKQQIKCDPIKHQQDWNTLKITEGLEAEKRYSEIGTFQAXXXXXXXXXXXXXXXXADIIKLTTNDSQVEKINEMWEKRINGVLRINMMRAITKKEPSVQRIPQIKIESEIIERMENVNLNNEDHNEPAMGSDVNRNIETRNQ 2020
MNNENSEKYCDYYQRPGHRSSKYHAQIECWNCGKLGHTATRCRVPKISFQCWQENHLP AYRTRRN+D+NNNTKT ESKSTEM+NEIN+ RMC+YL +QPHT+INQQSEI+VLQG SRKQQIKCDP+KHQQDWN LKITE LEAEKRYSEIGTFQARIEEE R+KEELLKADIIKLTTNDSQVEKINEMW KRINGV RINMMRAITKKEPSVQRIPQI+IES+IIERMENVNLNNEDHNEPA+GS+VNRNIETRNQ
Sbjct: 1 MNNENSEKYCDYYQRPGHRSSKYHAQIECWNCGKLGHTATRCRVPKISFQCWQENHLPTAYRTRRNNDENNNTKTTESKSTEMQNEINILTRMCSYLPDNQPHTEINQQSEIDVLQGMSRKQQIKCDPVKHQQDWNMLKITEALEAEKRYSEIGTFQARIEEESWSRKKEELLKADIIKLTTNDSQVEKINEMWAKRINGVPRINMMRAITKKEPSVQRIPQIRIESKIIERMENVNLNNEDHNEPAIGSEVNRNIETRNQ 261
BLAST of SMED30025868 vs. Planmine SMEST
Match:
SMESG000080940.1 (SMESG000080940.1)
HSP 1 Score: 450.284 bits (1157), Expect = 2.391e-150
Identity = 235/261 (90.04%), Postives = 247/261 (94.64%), Query Frame = 2
Query: 1238 MNNENSEKYCDYYQRPGHRSSKYHAQIECWNCGKLGHTATRCRVPKISFQCWQENHLPAAYRTRRNHDQNNNTKTPESKSTEMKNEINMPARMCNYLAVDQPHTKINQQSEINVLQGTSRKQQIKCDPIKHQQDWNTLKITEGLEAEKRYSEIGTFQAXXXXXXXXXXXXXXXXADIIKLTTNDSQVEKINEMWEKRINGVLRINMMRAITKKEPSVQRIPQIKIESEIIERMENVNLNNEDHNEPAMGSDVNRNIETRNQ 2020
MNNENSEKYCDYYQRP HRSSKYHAQIECWNCGKLGHTATRCR+PKISFQCWQENHLP AYRTRRNHDQNNNT+TPESKSTEM+NEIN+P RMC+YL +QPHT+INQQSEINVLQG SRKQQIK DPIKHQQDWNTLK+TE LEAEKRYSEI TFQARIEEER RRRKEELLKADIIKLTTNDSQVEKINEMWEKRIN + RINM+RAITKKEPSVQRIPQI+IESEIIERMENVNLNNEDHNEPA+ S VNRNIETRNQ
Sbjct: 1 MNNENSEKYCDYYQRPDHRSSKYHAQIECWNCGKLGHTATRCRIPKISFQCWQENHLPTAYRTRRNHDQNNNTETPESKSTEMQNEINIPTRMCSYLPDNQPHTEINQQSEINVLQGISRKQQIKWDPIKHQQDWNTLKMTEALEAEKRYSEIRTFQARIEEERWRRRKEELLKADIIKLTTNDSQVEKINEMWEKRINRIPRINMVRAITKKEPSVQRIPQIRIESEIIERMENVNLNNEDHNEPAIESYVNRNIETRNQ 261
BLAST of SMED30025868 vs. Planmine SMEST
Match:
SMESG000043095.1 (SMESG000043095.1)
HSP 1 Score: 445.277 bits (1144), Expect = 1.549e-147
Identity = 227/261 (86.97%), Postives = 241/261 (92.34%), Query Frame = 2
Query: 1238 MNNENSEKYCDYYQRPGHRSSKYHAQIECWNCGKLGHTATRCRVPKISFQCWQENHLPAAYRTRRNHDQNNNTKTPESKSTEMKNEINMPARMCNYLAVDQPHTKINQQSEINVLQGTSRKQQIKCDPIKHQQDWNTLKITEGLEAEKRYSEIGTFQAXXXXXXXXXXXXXXXXADIIKLTTNDSQVEKINEMWEKRINGVLRINMMRAITKKEPSVQRIPQIKIESEIIERMENVNLNNEDHNEPAMGSDVNRNIETRNQ 2020
MN ENSEKYCDYYQRPGHRSSKYH QIECWNCGKLGHTAT+CRVPKISFQCWQENHLP AYRTRRN+D+NNNTKT ESKSTEM+NE +MPARMC+YLA +QPH +INQQSEINVLQ S KQQIKCDPIKHQQDWNTLKITE LEAEKRYS++GTFQA IEEER R RKE+LLKADIIKLTTNDSQV+KINEMWEKRING+ RINMMRAIT KEPSVQRIPQI+IESEIIERMENVNLNN DHNEP SDVNRNIETRNQ
Sbjct: 1 MNTENSEKYCDYYQRPGHRSSKYHEQIECWNCGKLGHTATKCRVPKISFQCWQENHLPTAYRTRRNNDENNNTKTAESKSTEMQNEKDMPARMCSYLADNQPHMEINQQSEINVLQDISTKQQIKCDPIKHQQDWNTLKITEALEAEKRYSKMGTFQAYIEEERWRSRKEKLLKADIIKLTTNDSQVKKINEMWEKRINGLPRINMMRAITNKEPSVQRIPQIRIESEIIERMENVNLNNGDHNEPTTESDVNRNIETRNQ 261
The following BLAST results are available for this feature:
Sequences
The following sequences are available for this feature:
transcript sequence
>SMED30025868 ID=SMED30025868|Name=SMED30025868|organism=Schmidtea mediterranea sexual|type=transcript|length=2629bp back to top protein sequence of SMED30025868-orf-1
>SMED30025868-orf-1 ID=SMED30025868-orf-1|Name=SMED30025868-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=278bp
MNNENSEKYCDYYQRPGHRSSKYHAQIECWNCGKLGHTATRCRVPKISFQ back to top
