run_metadata: 28672
This data as json
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| 28672 | SRR26502062 | SRX22205816 | SRS19261224 | SRP468205 | PRJNA1031674 | Longitudinal gene expression profiling in Nodal induced and control zebrafish embryonic explants | GSE246158 | Transcriptome Analysis | We report RNA sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 N constitutively active Nodal receptor CA acvr1b* T and uninjected U controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere SR zfs:0000015 30 50% epiboly 50 shield SH 75% epiboly 75 90% epiboly 90 and 2 somite 2S corresponding to 4 4.7 5.3 6 8 9 and 11 hpf respectively. Overall design: Sequencing of polyadenylated mRNAs from ndr2 N CA acvr1b*T and uninjected U explants with 3 biological replicates A C per condition per stage SR 2S. | pubmed:39651654 | N 75 A | GSM7863818 | tissue:Zebrafish embryo explants|condition:Nodal ligand ndr2 N|developmental stage:75% epiboly 75|stage index:5|geo loc name:missing|collection date:missing | N 75 A | Sequenced reads were trimmed for adaptor sequence using TrimGalore Reads were mapped to the UCSC zebrafish reference genome danRer11 using STAR featureCounts was used to evaluate gene expression level as read counts Assembly: Danio rerio GRCz11 Ensembl Release 98 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample | Zebrafish embryo explants | Explants of N and T conditions were isolated from embryos injected at the 1 cell stage with 10 pg ndr2 or 0.5 pg CA acvr1b* mRNA respectively | Total RNA was isolated using Trizol reagent then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols | Explants were cultured in explant media from their time of isolation from the embryo at approximately 3 hours post until collection | condition:Nodal ligand ndr2 N|developmental stage:75% epiboly 75|approx time hpf index:5 | GSM7863818 | GSM7863818: N 75 A; Danio rerio; RNA Seq | GSM7863818 r1 | GSM7863818 | 1 | Total RNA was isolated using Trizol reagent then purified by sodium acetate precipitation and eluted in 10 mM Tris pH7.5 RNA libraries were prepared for sequencing using standard Illumina protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468205 | loader:fastq load.py | N_75_A_1.fq.gz N_75_A_2.fq.gz | fastq fastq | 7142931300.0 | 23809771.0 | GSM7863818 r1 | 0:150 1:150 | A:1937831740;C:1643617608;G:1644790568;T:1916566274;N:125110 | 150 | 150 | 1937831740 | 1643617608 | 1644790568 | 1916566274 | 125110 | SRX22205816 | SRS19261224 | SRA1738892 | Baylor College of Medicine | Baylor College of Medicine | 2 | 0.95756 | 0.95571 | 0.09626 | 0.09538 | 0.75568 | 0.75574 | 0.4801 | 0.48291 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2023-10-24 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures |