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| Status |
Public on May 12, 2024 |
| Title |
primary Leydig cells, tphp3 |
| Sample type |
SRA |
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| Source name |
testis
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| Organism |
Mus musculus |
| Characteristics |
tissue: testis
cell type: primary Leydig cells
genotype: WT
treatment: TPhP
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol. 2 ug of total RNA was used for the construction of sequencing libraries.
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.The PCR reaction system and program are configured and set up to amplify the product.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Description |
TPhP_3 FPKM
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| Data processing |
The raw data was filtered with SOAPnuke (v1.5.2) [1] by 1) Removing reads
containing adapters (adapter contamination); 2) Removing reads whose unknown base
('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio
(Base quality less than or equal to 15) is more than 50%, afterwards clean reads were
obtained and stored in FASTQ format.
Assembly: GRCm38.p6
Supplementary files format and content: xlsx. Files include FPKM values for each sample
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| Submission date |
May 07, 2024 |
| Last update date |
May 12, 2024 |
| Contact name |
Yuhan Ma |
| E-mail(s) |
maryuhon@outlook.com
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| Organization name |
Nanjing University
|
| Street address |
Hankou Road 22
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210093 |
| Country |
China |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE266861 |
Impact of triphenyl phosphate on sperm quality reduction: evidence from human, mice and cells |
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| Relations |
| BioSample |
SAMN41246369 |
| SRA |
SRX24482326 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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