run_metadata: 61827
This data as json
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| 61827 | SRR12998959 | SRX9450370 | SRS7663337 | SRP291417 | PRJNA675020 | The genome wide impact of nipblb loss of function on zebrafish gene expression | PRJNA675020 | Other | Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity such as the cohesin genes and their regulator NIPBL. In our previous studies using a zebrafish model for nipblb knock down we described the effect of nipblb loss of function in specific contexts such as central nervous system development and hematopoiesis. However the genome wide transcriptional impact of nipblb loss of function in zebrafish embryos at diverse developmental stages remains under investigated. By RNA seq analyses in zebrafish embryos at 24 hpf we examined genome wide effects of nipblb haploinsufficiency on transcriptional programs. Differential gene expression analysis revealed that nipblb loss of function has a major impact on gene expression at 24 hpf and that this massive transcriptional dysregulation is rescued by specific back up mechanisms that counteract the transcriptional patterns induced by nipblb silencing. Moreover we unraveled a connection between nipblb dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes enforcing our previous evidences on the involvement of NIPBL related transcriptional dysregulation in hematological malignancies. | total RNA from zebrafish embryos | CTRL 24h 3 | strain:AB|age:24 hpf stage:embryo|sex:not determined|tissue:embryos|biomaterial provider:Prof. Anna Pistocchi Dept. of Medical Biotechnology and Translational Medicine University of Milan|replicate:3|genotype:wild type|sample type:whole organism|store cond:immediate extration|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio control MO wild type at 24 hpf replicate 3 | Illumina CTRL 24h 3 | Illumina CTRL 24h 3 | RNA extracted from ctrl MO embryos at 24 hpf were used to prepare Illumina TruSeq Stranded mRNA Library then sequenced on Illumina HiSeq 4000 platform by paired end run | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP291417 | CTRL_24h_3_R1.fastq.gz CTRL_24h_3_R2.fastq.gz | fastq fastq | 11743125342.0 | 38884521.0 | CTRL 24h 3 R1.fastq.gz | 0:151 1:151 | A:3020506340;C:2830362106;G:2947603520;T:2944481126;N:172250 | 151 | 151 | 3020506340 | 2830362106 | 2947603520 | 2944481126 | 172250 | SRX9450370 | SRS7663337 | SRA1155106 | National Research Council (CNR)|Institute of Biomedical Technologies | National Research Council (CNR) Prof. Anna Pistocchi, Dept. of Medical Biotechnology and Translational Medicine -University of Milan | 2 | 0.95692 | 0.95604 | 0.05664 | 0.05614 | 0.67375 | 0.6786 | 0.4617 | 0.45912 | 151 | 151 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | Italy | 2020-11-06 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures |