run_metadata: 53641
This data as json
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| 53641 | SRR10004188 | SRX6742924 | SRS5293747 | SRP218844 | PRJNA560923 | Rbm24 functions as a critical translational regulator to pretect crystallin proteins accumulation for lens transparency. RNA seq data of 33 hpf rbm24a / and wildtype embryo head explant | GSE136003 | Transcriptome Analysis | This experiment is aimed to compare the transcriptomes of rbm24a mutant and wildtype at 33 hpf. As Rbm24a is an RNA binding protein this comparation is suitable to obtain information on differential gene expression and alternative splicing. We found that the expression of most of the crystallin genes and many other lens specific genes are down regulated in rbm24a mutant without xxx in splicing patterns. Overall design: It contains two groups: wildtype and rbm24a / . Wildtype was used as control | pubmed:32170011 | WT 1 | GSM4039261 | source name:head explant|dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB | WT 1 | Base calling: Bcl2fastq v2.17.1.14 Data filtering step: Cutadapt（version 1.9.1） Allignment: Hisat2v2.0.1 default parameter Differential gene expression: DESeq2（V1.6.3） Gene expression: Htseq software V 0.6.1 Genome build: GRCz11 Supplementary files format and content: excel file gene expression level in FPKM Supplementary files format and content: excel file differentially expressed genes | head explant | the head region of 33 hpf embryos were cut and collected for RNA extraction | Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al. 2017. | dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB | GSM4039261 | GSM4039261: WT 1; Danio rerio; RNA Seq | GSM4039261 | 1 | Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al. 2017. | GEO Accession:GSM4039261 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP218844 | WT1_combined_R1.fastq.gz WT1_combined_R2.fastq.gz | fastq fastq | 6916773600.0 | 23055912.0 | GSM4039261 r1 | 0:150 1:150 | A:1871554357;C:1578397354;G:1603789627;T:1862359143;N:673119 | 150 | 150 | 1871554357 | 1578397354 | 1603789627 | 1862359143 | 673119 | SRX6742924 | SRS5293747 | SRA945259 | GEO | School of Lifesciences, Shandong University | 2 | 0.92052 | 0.92653 | 0.07178 | 0.07144 | 0.72076 | 0.73312 | 0.46318 | 0.48078 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | China | 2019-08-19 | Pharyngula | Embryo | Head | Nervous System |