run_metadata: 26539
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 26539 | SRR26130976 | SRX21844391 | SRS18942406 | SRP462307 | PRJNA1019490 | Single Cell RNA seq of Zebrafish Hypothalamus | PRJNA1019490 | Other | Brain nuclei are traditionally defined by their anatomy activity and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions ranging from sleep and wakefulness to feeding stress and reward in all vertebrates. | 10X47 1 | breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 3|BioSampleModel:Model organism or animal | SC ZF Hypo3 | 10X47 1 | 10X47 1 | we worked swiftly with cold well oxygenated solutions optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations kept it fresh and oxygenated it. The zebrafish procedure began with lethal anesthesia brain dissection in ice cold aCSF embedding in 1.5% gel and vibratome sectioning. Tissue was dissociated in the Papain vial triturated filtered and washed followed by centrifugation. The pellet was resuspended in aCSF with DNase assessed for cell viability counted and diluted for use. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP462307 | 10X47_1_S1_L001_R1_001.fastq.gz 10X47_1_S1_L001_R2_001.fastq.gz 10X47_1_S1_L002_R1_001.fastq.gz 10X47_1_S1_L002_R2_001.fastq.gz 10X47_1_S1_L003_R1_001.fastq.gz 10X47_1_S1_L003_R2_001.fastq.gz 10X47_1_S1_L004_R1_001.fastq.gz 10X47_1_S1_L004_R2_001.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq | 3288490212.0 | 39148693.0 | 10X47 1 S1 L001 R1 001.fastq.gz | 0:28 1:56 | A:950740376;C:692224998;G:723085676;T:922337432;N:101730 | 28 | 56 | 950740376 | 692224998 | 723085676 | 922337432 | 101730 | SRX21844391 | SRS18942406 | SRA1717104 | Technion - Israel Institute of Technology|Neuroscince | Technion - Israel Institute of Technology | 2 | 0.01086 | 0.86383 | 0.0052 | 0.31674 | 0.98244 | 0.78309 | 0.39399 | 0.52299 | 28 | 56 | T | B | sc-like readlen | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_generic | generic-scrnaseq-only | Israel | 2023-09-21 | Adult | Adult | Brain | Nervous System |