run_metadata: 56514
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56514 | SRR10988547 | SRX7649997 | SRS6079494 | SRP246053 | PRJNA603897 | Comparsion of transcriptome between slbp1 mutant and wildtype sibling | GSE144517 | Transcriptome Analysis | The neurogenic state at transcriptomic level in delayed neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf. Overall design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced. | head 2d rw440 sib1 | GSM4289905 | source name:head|tissue:Head|age:2dpf | head 2d rw440 sib1 | Hiseq Control Software HD v3.4.0 used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 whole genome using hisat2 with parameters k 3 p 36 Raw count data was obtained by featureCounts with parameters p T 36 t exon g gene id a "GRCz11" cut f 1 7 12 Genome build: GRCz11 Supplementary files format and content: tab delimited text file includes raw count data for each sample in one file | head | Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:Head|age:2dpf | GSM4289905 | GSM4289905: head 2d rw440 sib1; Danio rerio; RNA Seq | GSM4289905 | 1 | Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4289905 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP246053 | 2d_rw440_sib1_R1.fastq.gz 2d_rw440_sib1_R2.fastq.gz | fastq fastq | 2654979688.0 | 8840507.0 | GSM4289905 r1 | 0:150.19 1:150.13 | A:624000299;C:675145222;G:678635011;T:676731946;N:467210 | 150 | 150 | 624000299 | 675145222 | 678635011 | 676731946 | 467210 | SRX7649997 | SRS6079494 | SRA1034453 | GEO | Developmental Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University | 2 | 0.9317 | 0.94861 | 0.06364 | 0.05753 | 0.72811 | 0.75055 | 0.50771 | 0.52256 | 151 | 151 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | Japan | 2020-01-30 | Hatching | Embryo | Head | Nervous System |