run_metadata: 24599
This data as json
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| 24599 | SRR25462248 | SRX21195033 | SRS18453959 | SRP452269 | PRJNA1000446 | Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish | GSE239623 | Transcriptome Analysis | Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau. | PV WT1 | GSM7669028 | source name:follicle|strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+|geo loc name:missing|collection date:missing | PV WT1 | Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file | follicle | TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina | strain:AB|tissue:follicle|developmental stage:pre vitellogenin|genotype:WT ybx1+/+ | GSM7669028 | GSM7669028: PV WT1; Danio rerio; RNA Seq | GSM7669028 r1 | GSM7669028 | 1 | TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP452269 | PV_WT1_R1.fastq PV_WT1_R2.fastq | fastq fastq | 3244660111.0 | 16481925.0 | GSM7669028 r1 | 0:98.44 1:98.42 | A:831426044;C:781489498;G:779991004;T:848549246;N:3204319 | 98 | 98 | 831426044 | 781489498 | 779991004 | 848549246 | 3204319 | SRX21195033 | SRS18453959 | Karp 12006A, Biology of Vascular Program, Boston Children's Hospital | 2 | 0.94779 | 0.95185 | 0.02328 | 0.02298 | 0.74294 | 0.74391 | 0.48052 | 0.47966 | 95 | 95 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | nebnext | bulk | bulk | bulk | United States | 2023-07-31 | Undetermined | Embryo | Gonad | Reproductive System |