run_metadata: 74668
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 74668 | SRR23928776 | SRX19738955 | SRS17105108 | SRP428413 | PRJNA947108 | Gene expression profile at single cell level of zebrafish trunk from WT or flt1 mutant 3dpf. | GSE227806 | Transcriptome Analysis | scRNA seq was used to investigate neurovascular cross talk in zebrafish trunk. Overall design: Zebrafish trunk of WT and flt1 mutant were dissected dissociated and processed for single cell RNA Seq using 10X Genomics Chromium droplet based system | parent bioproject:PRJNA947103 | pubmed:38600061 | flt1mut replicate 2 scRNAseq trunk | GSM7108419 | source name:Trunk|tissue:Trunk|genotype:flt1ka604|age:3dpf|geo loc name:missing|collection date:missing | flt1mut replicate 2 scRNAseq trunk | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCZ11 v107 Supplementary files format and content: matrix files | Trunk | Zebrafish embryos 3dpf were anesthethised with Tricain prior the dissection of the trunk. Dissected trunks were dissociated using a mix of 0.25% Trypsin and collagenase 4mg/mL centrifuged to collect the cells resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris. Cells were washed and resuspend in PBS prior 10X genomic experiment Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics | tissue:Trunk|genotype:flt1ka604|age:3dpf | GSM7108419 | GSM7108419: flt1mut replicate 2 scRNAseq trunk; Danio rerio; RNA Seq | GSM7108419 r1 | GSM7108419 | 1 | Zebrafish embryos 3dpf were anesthethised with Tricain prior the dissection of the trunk. Dissected trunks were dissociated using a mix of 0.25% Trypsin and collagenase 4mg/mL centrifuged to collect the cells resuspended into DMEM + 10% Fetal Bovine Serum and filtered to remove the debris. Cells were washed and resuspend in PBS prior 10X genomic experiment Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP428413 | loader:fastq load.py | AAAVLTHHV_trunk_flt1_pool_22s004695-1-1_PREAU_lane1MUT2_1_sequence.txt AAAVLTHHV_trunk_flt1_pool_22s004695-1-1_PREAU_lane1MUT2_2_sequence.txt | fastq fastq | 35418985138.0 | 300160891.0 | GSM7108419 r1 | 0:28 1:90 | A:9637251760;C:8083980683;G:8336318307;T:9349259129;N:12175259 | 28 | 90 | 9637251760 | 8083980683 | 8336318307 | 9349259129 | 12175259 | SRX19738955 | SRS17105108 | SRA1608738 | Karlsruhe Institute of Technology (KIT) | Karlsruhe Institute of Technology (KIT) | 2 | 0.00564 | 0.94991 | 0.00167 | 0.10681 | 0.99088 | 0.78904 | 0.41428 | 0.4583 | 28 | 90 | T | B | sc-like readlen | illumina | nextseq_v2 | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-03-21 | Larval | Larval | Trunk | Surface Structure |