run_metadata: 68220
This data as json
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| 68220 | SRR17676758 | SRX13840238 | SRS11717441 | SRP355951 | PRJNA798905 | Effect of zinc on zerafish brain | GSE194049 | Transcriptome Analysis | We evaluated the effect of zinc on zebrafish brain via single cell analysis Overall design: Evaluate the effect of zinc on zebrafish brain via single cell analysis | Zn15 Brain | GSM5827020 | source name:Zn15 Brain Single cell|tissue:Brain|treatment:Zn15 | Zn15 Brain | Qualitycontrol We use fastp to perform basic statistics on the quality of the raw reads. Generally cellranger count support FASTQ files from raw base call BCL files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence. Generation and Analysis of Single Cell Transcriptomes Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline https://support.10xgenomics.com/single cell geneexpression/software/pipelines/latest/what is cell ranger using default parameters. All downstream single cell analyses were performed using Cell Ranger and Seurat Macosko et al. 2015; Satija et al. 2015 unless mentioned specifically. In brief for each gene and each cell barcode filtered by CellRanger unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction clustering and gene expression algorithms using cellranger default parameter settings Genome build: GRCz11 Supplementary files format and content: barcodes counts barcodes and gene files | Zn15 Brain Single cell | Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols | tissue:Brain|treatment:Zn15 | GSM5827020 | GSM5827020: Zn15 Brain; Danio rerio; RNA Seq | GSM5827020 r1 | GSM5827020 | 1 | Single brain cell were prepared libraries were prepared for sequencing using standard 10Xgenomic protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP355951 | Zinc_1.5-1_S1_L004_R1_001.fastq.gz Zinc_1.5-1_S1_L004_R2_001.fastq.gz | fastq fastq | 1539071400.0 | 5130238.0 | GSM5827020 r1 | 0:150 1:150 | A:658313518;C:244042507;G:225665242;T:410991023;N:59110 | 150 | 150 | 658313518 | 244042507 | 225665242 | 410991023 | 59110 | SRX13840238 | SRS11717441 | SRA1359549 | Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization | Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization | 2 | 0.0 | 0.82858 | 0.0 | 0.53324 | 1.0 | 0.79498 | 0.4737 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2022-01-20 | Undetermined | Undetermined | Brain | Nervous System |