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| Status |
Public on Jun 01, 2018 |
| Title |
WT_4 |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 6 months
genotype: Wild type
tissue: ovary
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| Treatment protocol |
Mice used for the experiment were initially primed with PMSG at the dose of 5 IU/mouse. Forty-six hours later, they were euthanized, and their ovariaies were collected and lysed in 350ul RLT buffer for RNA extraction.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy Mini Kit (Qiagen, Germantown, MD, USA) according to manufacturer's instructions, and 500 ng was then taken out from each of them and subjected to mRNA isolation using NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB, Ipswich, MA, USA).
The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
WT_201
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| Data processing |
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.13)
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized usingcuffnorm. Differentially expressed genes are calculated using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
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| Submission date |
May 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
You-Qiang Su |
| E-mail(s) |
youqiang.su@njmu.edu.cn
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| Organization name |
Nanjing Medical University
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| Department |
State Key Laboratory of Reproductive Medicine
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| Street address |
140 Hanzhong Road
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210029 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE98497 |
Comparing the Transcriptomes of Wild Type and Mtor-Gdf9-Cre mediated Oocyte-Conditional Knockout Mouse ovaries by RNA-Seq Analysis |
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| Relations |
| BioSample |
SAMN06885922 |
| SRA |
SRX2780353 |
| 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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