run_metadata: 29260
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 29260 | SRR27336918 | SRX23013777 | SRS19977074 | SRP479907 | PRJNA1056454 | miR214 regulates sex determination through gsdf in zebrafish | PRJNA1056454 | Other | Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination. | CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP | miR214 PaternalKO gonads 31dpf rep1 | miR214 PaternalKO gonads 31dpf rep1 | strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal | = xlfn.CONCAT"mrna sequencing of zebrafish: " A10 | miR214 PaternalKO gonads 31dpf rep1 | miR214 PaternalKO gonads 31dpf rep1 | NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | ILLUMINA | NextSeq 500 | SRP479907 | miR214_PaternalKO_gonads_31dpf_rep1.fastq.gz | fastq | 2500978452.0 | 29773553.0 | miR214 PaternalKO gonads 31dpf rep1.fastq.gz | 0:84 | A:646162933;C:593855971;G:578265372;T:682684551;N:9625 | 84 | 646162933 | 593855971 | 578265372 | 682684551 | 9625 | SRX23013777 | SRS19977074 | SRA1775014 | Rene Ketting group|Ketting Lab | Rene Ketting group | 1 | 0.95147 | 0.05972 | 0.69071 | 0.47043 | 84 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | trueseq | bulk | unknown | unknown | Germany | 2023-12-24 | Larval | Larval | Gonad | Reproductive System |