{"database": "metadata", "table": "run_metadata", "rows": [[55641, "SRR10586525", "SRX7266917", "SRS5761460", "SRP234691", "PRJNA593445", "A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA Seq]", "GSE141427", "Transcriptome Analysis", "Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf  24hpf and 44hpf zebrafish hindbrains were used for single cell RNA sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity  dorso ventral patterning  boundary and centre progenitor cells and temporal regulation of neurogenesis. Overall design: 16hpf  24hpf  44hpf hindbrains were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina HiSeq 4000.", "parent bioproject:PRJNA593433", "pubmed:32094115", null, "24hpf Hindbrain scRNA seq", "GSM4202681", null, "source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5\u00b0C", "24hpf Hindbrain scRNA seq", "10X\u2019s Cell Ranger software was used to de multiplex Illumina BCL output  create fastq files and generate single cell feature counts for each library Three 10X libraries representing the 16hpf  24hpf and 44hpf stages of embryonic development were aggregated using the 10X software \u201ccellranger aggr\u201d function  which sub samples reads such that all libraries have the same effective sequencing depth. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file containing aggregated Cell Ranger counts", "Dissected hindbrain and surrounding tissues", null, "Embryos were decorionated and deyolked in DMEM with high Glucose  no Glutamine  no Calcium 11530556  Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100  Amsbio supplemented with 1mg/ml Papain 10108014001  Sigma for 25min at 37\u00b0C and resuspended one time during incubation; cells were then transferred to HBSS no calcium  no magnesium  no phenol red; 11140035  ThermoFisher Scientific supplemented with 5%FBS  rock inhibitor Y 27632  Stem Cell Technologies  and 1X non essential amino acids 11140035  ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20\u00b5m strainers 130 101 812  Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233  10X Genomics; 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