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| Status |
Public on Sep 06, 2023 |
| Title |
ovary, BPA treated, biol rep1 |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Oryzias latipes |
| Characteristics |
tissue: ovary
treatment: BPA
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| Extracted molecule |
total RNA |
| Extraction protocol |
The ovary of control and BPA lineage female fish (15 individuals from each lineage) were used for total RNA extraction by using Quick RNA/DNA Miniprep Plus Kit (#D-7003, Zymo Research, CA, USA) according to the manufacturer's protocol
The RNA of the ovary from three females were pooled as one biological replicate and there were three biological replicates per group. Transcriptome libraries were prepared using NEBNext Ultra II RNA Kit and manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
B1
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| Data processing |
The reads were first preprocessed with fastp (v 0.23.2), an ultra-fast all-in-one FASTQ preprocessor, which does quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data
The fastp-processed reads were then mapped on medaka genome (Oryzias_latipes.ASM223467v1) using STAR (2.7.7a)
Finally, DESeq2 (v1.34.0) was used to do the differential expression analysis
Assembly: Oryzias_latipes.ASM223467v1
Supplementary files format and content: pcos_rnaseq_normExp_diffExp_filtered-Padj.tsv : Normalized log2 expression values for all samples in tab-delimited text-file
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| Submission date |
Feb 28, 2023 |
| Last update date |
Sep 06, 2023 |
| Contact name |
Ramji Bhandari |
| E-mail(s) |
bhandarir@missouri.edu
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| Organization name |
University of Missouri
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| Department |
Division of Biological Sciences
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| Lab |
Lefevre 219
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| Street address |
1200 University Ave
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| City |
Columbia |
| State/province |
MO |
| ZIP/Postal code |
65211 |
| Country |
USA |
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| Platform ID |
GPL25587 |
| Series (1) |
| GSE226322 |
Transcriptional analysis reveals the progression of PCOS to ovarian cancer in medaka fish ancestrally exposed to BPA |
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| Relations |
| BioSample |
SAMN33524282 |
| SRA |
SRX19530651 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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