run_metadata: 48774
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 48774 | SRR7297839 | SRX4200373 | SRS3410607 | SRP150365 | PRJNA475784 | Phenotypic landscape of schizophrenia associated genes defines candidates and their shared functions | GSE115427 | Transcriptome Analysis | Znf536 mutant and wild types were profiled to discover cell type landscape modulated by the transcription factor. Overall design: 10x libraries of single cell transcriptomes | pubmed:30929901 | znf mut 10x | GSM3187949 | source name:zebrafish brain|tissue:Forebrain|developmental stage:6dpf|genotype/variation:znf mutant | znf mut 10x | Raw sequencing data was converted to matrices of expression using the cell ranger software provide by 10x genomics. Raw BCL files from Illumina nextseq were demultiplexed into paired end gzip compressed FASTQ files using cellranger mkgastq. Both FASTQs were then provided as input to cell ranger count which partitioned reads into cell of origin based on a 16 bp barcode on the left read. Reads were aligned to a zebrafish reference transcriptomeENSEMBL Zv10 release 82 reference transcriptome and transcript counts quantified for each annotated gene. 10bp UMI on th eleft read was used to collapse PCR duplicates. Genome build: GRCz10 Supplementary files format and content: CSV files for transcriptome data were generated using the cellranger pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for gene. | zebrafish brain | Single cell suspensions were processsed according to manufacturer's instructions by 10X chromium 10x chromium | tissue:Forebrain|developmental stage:6dpf|genotype/variation:znf mutant | GSM3187949 | GSM3187949: znf mut 10x; Danio rerio; RNA Seq | GSM3187949 | 1 | Single cell suspensions were processsed according to manufacturer's instructions by 10X chromium 10x chromium | GEO Accession:GSM3187949 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP150365 | mut_possorted_genome_bam.bam | 10X Genomics bam file | 16531944740.0 | 285033530.0 | GSM3187949 r1 | 0:58 | A:5037043538;C:3032099047;G:3558921957;T:4900111360;N:3768838 | 58 | 5037043538 | 3032099047 | 3558921957 | 4900111360 | 3768838 | SRX4200373 | SRS3410607 | SRA720602 | GEO | Schier Lab, Molecular and Cellular Biology, Harvard University | 1 | 0.88667 | 0.33708 | 0.83102 | 0.50699 | 58 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2018-06-12 | Larval | Larval | Brain | Nervous System |