run_metadata: 35614
This data as json
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| 35614 | SRR32928245 | SRX28203072 | SRS24552778 | SRP575522 | PRJNA1244443 | An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing | PRJNA1244443 | Other | Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages. | Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method. | expt2.broad.48.bead.P18.B01.fq.gz | seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal | sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf bead dissociation replicate 3 | 81 | 81 | Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq. | OTHER | TRANSCRIPTOMIC SINGLE CELL | other | SINGLE | ILLUMINA | NextSeq 2000 | SRP575522 | expt2.broad.48.bead.P18.B01.fq.gz | fastq | 6255144.0 | 74466.0 | expt2.broad.48.bead.P18.B01.fq.gz | 0:84 | A:1953811;C:1213806;G:1335743;T:1748533;N:3251 | 84 | 1953811 | 1213806 | 1335743 | 1748533 | 3251 | SRX28203072 | SRS24552778 | SRA2104467 | University of Washington|Genome Sciences | University of Washington | B | usable mapping rate | illumina | nextseq_v2 | unknown | other | unknown | sc | single_cell_generic | generic-scrnaseq-only | United States | 2025-03-31 | Hatching | Embryo | Whole Organism | All anatomical structures |