run_metadata: 55638
This data as json
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| 55638 | SRR10586528 | SRX7266960 | SRS5761494 | SRP234692 | PRJNA593444 | A single cell transcriptome atlas of the developing zebrafish hindbrain [Fgf20a] | GSE141425 | Transcriptome Analysis | RNA seq profile of Fgf20a homozygous mutant hindbrains compared with wilde type hindbrains Method: 24hpf hindbrains were microdissected and the RNA was extracted. Qulity of dissection was monitored by qPCR and samples were selected for sequencing Overall design: 4 control wt Cnt and 3 Fgf20aHOM were deep sequenced | parent bioproject:PRJNA593433 | pubmed:32094115 | Cnt 2 | GSM4202666 | source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C | Cnt 2 | Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31 RSEM estimated gene level counts were rounded to integers Genome build: GRCz10 Supplementary files format and content: Tab delimited counts matrix with row representing genes and columns representing samples. | Dissected hindbrain and surrounding tissues | 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; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation. | tissue:Dissected hindbrain and surrounding tissues|Stage:24hpf|strain:LondonAB|genotype:wt|growth:28.5°C | GSM4202666 | GSM4202666: Cnt 2; Danio rerio; RNA Seq | GSM4202666 | 1 | 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; RNA was isolated using Quick RNA Microprep kit Zymo Research Samples were prepared with the Ovation® RNA Seq System V2 7102 NuGEN for cDNA amplification followed by NexteraXT Illumina for library preparation. | GEO Accession:GSM4202666 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP234692 | MT_C2_1.fastq.gz MT_C2_2.fastq.gz | fastq fastq | 13384473450.0 | 89229823.0 | GSM4202666 r1 | 0:75 1:75 | A:3648519008;C:3057477428;G:3043763915;T:3633023284;N:1689815 | 75 | 75 | 3648519008 | 3057477428 | 3043763915 | 3633023284 | 1689815 | SRX7266960 | SRS5761494 | SRA1006558 | GEO | The Francis Crick Institute | 2 | 0.93086 | 0.93239 | 0.06636 | 0.07075 | 0.73026 | 0.74221 | 0.47916 | 0.47798 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United Kingdom | 2019-12-04 | Pharyngula | Embryo | Brain | Nervous System |