run_metadata: 24589
This data as json
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| 24589 | SRR25462257 | SRX21195044 | SRS18453970 | SRP452270 | PRJNA1000445 | CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption | GSE239622 | Transcriptome Analysis | CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established 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. | PG HE 50dpf 2 | GSM7669020 | source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing | PG HE 50dpf 2 | 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:primary growth|age:50dpf|genotype:HE cdkn1a +/ | GSM7669020 | GSM7669020: PG HE 50dpf 2; Danio rerio; RNA Seq | GSM7669020 r1 | GSM7669020 | 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 | SRP452270 | PG_HE_2_S25_L003_R2_001.fastq.gz PG_HE_2_S25_L003_R1_001.fastq.gz | fastq fastq | 3915471868.0 | 19847479.0 | GSM7669020 r1 | 0:98.64 1:98.64 | A:982714666;C:957212118;G:961590362;T:1003408448;N:10546274 | 98 | 98 | 982714666 | 957212118 | 961590362 | 1003408448 | 10546274 | SRX21195044 | SRS18453970 | Karp 12006A, Biology of Vascular Program, Boston Children's Hospital | 2 | 0.93184 | 0.93552 | 0.01275 | 0.01275 | 0.78356 | 0.7835 | 0.49472 | 0.48841 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | nebnext | bulk | bulk | bulk | United States | 2023-07-31 | Juvenile | Juvenile | Gonad | Reproductive System |