run_metadata: 30508
This data as json
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| 30508 | SRR27764648 | SRX23429609 | SRS20284060 | SRP486518 | PRJNA1070582 | Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition | GSE254439 | Transcriptome Analysis | Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However developing tissues also undergo dynamic morphogenesis which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing GFP+ cells or ßcatCA unexpressing GFP cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq. | pubmed:39546611 | Mosaic GFP control GFP min lot2 | GSM8042248 | source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing | Mosaic GFP control GFP min lot2 | Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm. | early embryonic cell | Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol. | strain:AB|tissue:early embryonic cell|developmental stage:9 hpf | GSM8042248 | GSM8042248: Mosaic GFP control GFP min lot2; Danio rerio; RNA Seq | GSM8042248 r1 | GSM8042248 | 1 | Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 1500 | SRP486518 | Mosaic_GFP_control_GFP_min_lot2.fastq.gz | fastq | 7474464.0 | 207624.0 | GSM8042248 r1 | 0:36 | A:1796571;C:1274347;G:1548876;T:2854637;N:33 | 36 | 1796571 | 1274347 | 1548876 | 2854637 | 33 | SRX23429609 | SRS20284060 | SRA1793856 | Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University | Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University | 1 | 0.82922 | 0.20207 | 0.86143 | 0.54661 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | celseq | Japan | 2024-01-29 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures |