run_metadata: 65983
This data as json
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| 65983 | SRR19264691 | SRX15325092 | SRS13103752 | SRP335733 | PRJNA760904 | R loop landscapes during parental to zygotic transition in zebrafish | GSE183453 | Other | The R loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here we developed a novel R loop profiling technique ULI ssDRIP seq to decte global R loops from a limited number of cells. Based on this method we profiled the R loop landscapes during parental to zygotic transition and early development regulatory in zebrafish and revealed a series of important characters of R loops. Overall design: ULI ssDRIP seq development and R loop profiling in zebrafish | pubmed:38974143 | Zebrafish GFP dome RNA seq Rep1 | GSM6165454 | source name:dome|tissue:dome|genotype:Wild type|treatment:GFP injection | Zebrafish GFP dome RNA seq Rep1 | Basecalls were performed using bcl2fastq v2.17 for Novaseq output. Sequence reads were trimmed for adaptor sequence/low quality sequence using TrimGalore version 0.6.7. Trimmed sequence reads were mapped to danRer7 using HISTAT2 version 2.2.1 with default parameters. Raw counts for the feature of genes were extracted by featureCounts version 2.0.3. BigWig files were generated by using deepTools version 2.4.2 Assembly: danRer7 Supplementary files format and content: bw | dome | Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations. | tissue:dome|genotype:Wild type|treatment:GFP injection | GSM6165454 | GSM6165454: Zebrafish GFP dome RNA seq Rep1; Danio rerio; RNA Seq | GSM6165454 | 1 | Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations. | GEO Accession:GSM6165454 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP335733 | loader:fastq load.py | GFP-dome_RNA-seq_Rep1_1.fq.gz GFP-dome_RNA-seq_Rep1_2.fq.gz | fastq fastq | 6852929700.0 | 22843099.0 | GSM6165454 r1 | 0:150 1:150 | A:1807624022;C:1621249807;G:1628581234;T:1795363171;N:111466 | 150 | 150 | 1807624022 | 1621249807 | 1628581234 | 1795363171 | 111466 | SRX15325092 | SRS13103752 | SRA1289147 | GEO | Tsinghua University | 2 | 0.95097 | 0.95068 | 0.06105 | 0.0608 | 0.74485 | 0.74464 | 0.48655 | 0.49028 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | nebnext | bulk | unknown | unknown | China | 2022-05-18 | Blastula | Embryo | Undetermined | Embryo Imprecise |