run_metadata: 67814
This data as json
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| 67814 | SRR17313507 | SRX13490114 | SRS11385977 | SRP352175 | PRJNA791684 | Translational profiling of zebrafish retina cells using translating ribosome affinity purification methods | GSE192511 | Other | Translating ribosome affinity purification TRAP methods allow cell specific recovery of polyribosome associated RNAs by genetic tagging of ribosomes in selected cell populations. In this study we purified and analysed the polyribosome associated RNA fraction of zebrafish embryo´s retinas at 22 hpf To this aim we generated a transgenic strain in which the tagged ribosomes expression is restricted to the retina cells due to the activity of a specific promoter. Overall design: Analysis of ribosome associated mRNAs in zebrafish retina cells | pubmed:35174174 | Vsx2:TRAP 22hpf 3 | GSM5750326 | tissue:Vsx2:TRAP|strain:Vsx2:TRAP|developmental stage:22 hpf embryos only retina cells tagged | Vsx2:TRAP 22hpf 3 | Base calling performed using HiSeq Control Software 2.2.58 Quality of reads was checked using FastQC v.0.72 Reads were aligned to Danio rerio GRCz11 genome assembly using Hisat2 with default parameters v. 2.2.1 Raw counts of reads were obtained through the featureCounts software using the zebrafish genome GRCz11 annotation from Ensembl Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample | Vsx2:TRAP | Tagged ribosomes with mRNA attached to them were purified through inmunoprecipitation. postwards the RNA was isolated. RNA libraries were prepared for sequencing using standard Illumina protocols | strain:Vsx2:TRAP|developmental stage:22 hpf embryos only retina cells tagged | GSM5750326 | GSM5750326: Vsx2:TRAP 22hpf 3; Danio rerio; RNA Seq | GSM5750326 r1 | GSM5750326 | 1 | Tagged ribosomes with mRNA attached to them were purified through inmunoprecipitation. postwards the RNA was isolated. RNA libraries were prepared for sequencing using standard Illumina protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP352175 | TRAP3_00523AAA_GTGGCC_read1.fastq.gz TRAP3_00523AAA_GTGGCC_read2.fastq.gz | fastq fastq | 8792826250.0 | 35171305.0 | GSM5750326 r1 | 0:125 1:125 | A:1760289035;C:2642082686;G:2620444494;T:1768120361;N:1889674 | 125 | 125 | 1760289035 | 2642082686 | 2620444494 | 1768120361 | 1889674 | SRX13490114 | SRS11385977 | SRA1347903 | CABD | CABD | 2 | 0.9712 | 0.97179 | 0.28473 | 0.27911 | 0.96327 | 0.96341 | 0.84082 | 0.81514 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | Spain | 2021-12-22 | Segmentation | Embryo | Eye | Sensory System |