run_metadata: 25324
This data as json
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| 25324 | SRR25820349 | SRX21542119 | SRS18751470 | SRP457651 | PRJNA1010830 | Identifying hand2 downstream targets in cardiomyocyte during early cardiogenesis | GSE241971 | Other | hand2 reporter expressing cardiac cells fail to migrate to the midline. To investigate the underlying molecular changes we sequenced mRNA from 3900 and 3836 hand2 reporter expressing single cells from 24 hpf hand2 FLD / and hand2 FLD+/? sibling embryos respectively. Furthermore hand2 is broadly expressed within the LPM which gives rise to various cell lineages and tissues including the cardiovascular system blood kidneys mesothelium and limb connective tissue. To further investigate the requirement of Hand2 in the early events of cardiac lineage specification in zebrafish we aim to characterize the early hand2 expressing cardiac precursors by using embryonic CM H3K27ac ChIP seq and ATAC seq data. Overall design: scRNA seq: WT: hand2 reporter expressing single cells from 24 hpf hand2 FLD+/? Embryos; mutants: hand2 reporter expressing single cells from 24 hpf hand2 FLD / sibling embryos. ATAC seq and CGIP seq: Comparing myl7:GFP+ CMs with myl7:GFP cells | pubmed:39658721 | MUT replicate1 scRNA | GSM7746945 | source name:whole embryo|tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:hand2 mutants|geo loc name:missing|collection date:missing | MUT replicate1 scRNA | demultiplexing star solo mapping: ' soloType CB UMI Simple soloBarcodeReadLength 0 soloCellFilter EmptyDrops CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000' Assembly: danio rerio/101 Supplementary files format and content: 10x based mtx raw count matrix barcodes and genes | whole embryo | 10xGenomics | tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:hand2 mutants | GSM7746945 | GSM7746945: MUT replicate1 scRNA; Danio rerio; RNA Seq | GSM7746945 r1 | GSM7746945 | 1 | 10xGenomics | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP457651 | Yanli_10x_Mut_24hpf_R2.fastq.gz Yanli_10x_Mut_24hpf_R1.fastq.gz | fastq fastq | 12703207777.0 | 159786155.0 | GSM7746945 r1 | 0:28 1:51.50 | A:3417159154;C:2758515982;G:2823785724;T:3638099229;N:65647688 | 28 | 51 | 3417159154 | 2758515982 | 2823785724 | 3638099229 | 65647688 | SRX21542119 | SRS18751470 | SRA1702565 | Max Planck Institute for Heart and Lung Research | Max Planck Institute for Heart and Lung Research | 2 | 0.00189 | 0.93843 | 0.0006 | 0.12822 | 0.99571 | 0.781 | 0.38429 | 0.49855 | 28 | 52 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_generic | generic-scrnaseq-only | Germany | 2023-08-30 | Undetermined | Embryo | Whole Organism | All anatomical structures |