run_metadata: 63003
This data as json
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| 63003 | SRR13565172 | SRX9963416 | SRS8137083 | SRP303505 | PRJNA695273 | Single cell response landscape of graded Nodal signaling in zebrafish explants [bulk RNA seq] | GSE165652 | Transcriptome Analysis | Purpose: To identify nodal downsream target genes Methods: 0pg 2pg 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide CHX treated explants were collected at xxxhpf 5hpf and 6hpf for bulk RNA seq Results: We found 105 Nodal targets p value <0.05 padj < 0.1 log2 fold change >= 1 Conclusions: 105 Nodal targets were identified Overall design: zebrafish explants injected with ndr2 mRNA | parent bioproject:PRJNA695267 | pubmed:37729057 | zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep2 | GSM5047600 | source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA | zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep2 | The sequencing reads were aligned to the zebrafish GRCz11 genome using STAR and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package. Genome build: GRCz11 Supplementary files format and content: comma delimited csv files included read counts of each sample and each gene | zebrafish cells | 10pg 6pg 2pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. Uninjected embryos were used as Control.For the samples injected with 10pg ndr2 mRNA 20min post the injection half of the samples were treated with Cycloheximide 50μg/μl MCE CAS No. 66 81 9 until harvest. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 4hpf 5hpf 6hpf corresponding to embryonic developmental stage separately. | Total RNAs was extracted using TRIzol following the manufacturer’s instruction RNA libraries were prepared for sequencing using standard Illumina protocols | explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium | strain:AB|tissue:embryonic cells|age:6hpf|treatment:injected with 10pg ndr2 mRNA | GSM5047600 | GSM5047600: zebrafish explants injected with 10pg ndr2 mRNA 6hpf rep2; Danio rerio; RNA Seq | GSM5047600 | 1 | Total RNAs was extracted using TRIzol following the manufacturer's instruction RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM5047600 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP303505 | wt_cyc_50_6h_2_FRAS190066753-1a_1.clean.fq.gz wt_cyc_50_6h_2_FRAS190066753-1a_2.clean.fq.gz | fastq fastq | 8468408100.0 | 28228027.0 | GSM5047600 r1 | 0:150 1:150 | A:2252327754;C:1995087946;G:2004951478;T:2215944168;N:96754 | 150 | 150 | 2252327754 | 1995087946 | 2004951478 | 2215944168 | 96754 | SRX9963416 | SRS8137083 | SRA1188620 | GEO | Institute of genetics, Zhejiang University | 2 | 0.95119 | 0.94983 | 0.06689 | 0.06701 | 0.76404 | 0.76469 | 0.47462 | 0.47055 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | China | 2021-01-27 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures |