run_metadata: 30745
This data as json
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| 30745 | SRR28346492 | SRX23952997 | SRS20753492 | SRP495277 | PRJNA1088100 | Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo | GSE261604 | Transcriptome Analysis | To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500. | parent bioproject:PRJNA926354 | pubmed:39395410 | AVC DMSO scRNAseq | GSM8147317 | source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing | AVC DMSO scRNAseq | The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample | Heart | Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark. | Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1. | tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO | GSM8147317 | GSM8147317: AVC DMSO scRNAseq; Danio rerio; RNA Seq | GSM8147317 r1 | GSM8147317 | 1 | Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP495277 | loader:fastq load.py | AVC_Ctrl_S1_L004_I1_001.fastq.gz AVC_Ctrl_S1_L004_I2_001.fastq.gz AVC_Ctrl_S1_L004_R1_001.fastq.gz AVC_Ctrl_S1_L004_R2_001.fastq.gz | fastq fastq fastq fastq | 7430049030.0 | 53840935.0 | GSM8147317 r4 | 0:10 1:10 2:28 3:90 | A:1337094348;C:1142353903;G:1151539276;T:1214006711;N:689912 | 10 | 10 | 28 | 90 | 1337094348 | 1142353903 | 1151539276 | 1214006711 | 689912 | SRX23952997 | SRS20753492 | SRA1824323 | Department of Pharmacology, Yamagata University | Department of Pharmacology, Yamagata University | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Japan | 2024-03-14 | Juvenile | Juvenile | Heart | Cardiovascular System |