run_metadata: 31843
This data as json
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| 31843 | SRR28709007 | SRX24276186 | SRS21041150 | SRP502090 | PRJNA1101048 | Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish | GSE264143 | Transcriptome Analysis | Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67. | dpf47 Ov mt 3 | GSM8212802 | source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing | dpf47 Ov mt 3 | Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample. | Ovary | Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. | WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food. | tissue:Ovary|age:dpf 47|genotype:mutant | GSM8212802 | GSM8212802: dpf47 Ov mt 3; Danio rerio; RNA Seq | GSM8212802 r1 | GSM8212802 | 1 | Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP502090 | loader:fastq load.py | NS51397.C33_20230510_103430.L001.1.fastq.gz NS51397.C33_20230510_103430.L001.2.fastq.gz | fastq fastq | 8256087174.0 | 27338037.0 | GSM8212802 r1 | 0:151 1:151 | A:2217123657;C:1857924925;G:2109544983;T:2069850323;N:1643286 | 151 | 151 | 2217123657 | 1857924925 | 2109544983 | 2069850323 | 1643286 | SRX24276186 | SRS21041150 | SRA1847037 | Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences | Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences | B | B | biological fallback assumption | illumina | nextseq | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2024-04-16 | Juvenile | Juvenile | Gonad | Reproductive System |