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| Status |
Public on Jun 09, 2021 |
| Title |
control_1 |
| Sample type |
SRA |
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| Source name |
Sertoli cells
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| Organism |
Rattus norvegicus |
| Characteristics |
genotype: control group
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the Sertoli cells using Trizol (Invitrogen, Carllsbad, CA, USA ) according to the manual instructions .The mix was centrifuge at 12000xg for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000xg for 10min at 4°C, the aqueous phase was transferred to a new 1.5 ml tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000 xg for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25µL~100µL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop (NanoDrop, Madison, USA) and Agilent 2100 bioanalyzer (Agilent, Santa Clara, USA).
Take 200ng total RNA samples (only for human or mouse) and use RNase H to remove the rRNA. DNase I digested double-stranded and single-stranded DNA presenting in RNA samples. mRNA molecules were fragmented into small pieces using fragmentation reagent. First-strand cDNA was generated by First Strand Master Mix and Super Script II reverse transcription, then add Second Strand Master Mix to synthesize the second-strand cDNA. Purify the DNA with Ampure XP Beads, then carry out end repair. The end-repaired products were purified by magnetic beads and re-dissolved in EB Solution. The purified fragmented cDNA was combined with A-Tailing Mix, and incubated. Then combine the Adenylate 3'Ends DNA, RNA Index Adapter and Ligation Mix, incubate. Purify the product DNA with Ampure XP Beads. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix were performed to enrich the cDNA fragments. Then the PCR products were purified with Ampure XP Beads. The libraries were assessed quality and quantity in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The qualified libraries were amplified on cBot to generate the cluster on the flowcell. And the amplified flowcell will be sequenced single end on the HiSeq X-ten paltform (BGI-Shenzhen, China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
BBMAP used for triming reads. It can binning reads based on mapping to multiple references at once
Mapping sequencing RNA reads to align genome assembly using sofeware Hisat2
DEseq2 used to analyze the difference expression of lncRNA, circRNA, mRNA
Supplementary_files_format_and_content: tab-delimited text files include the number of reads relative RPKM values, and P-values for control and experimental group Sample.
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| Submission date |
Feb 28, 2021 |
| Last update date |
Jun 09, 2021 |
| Contact name |
wenjie liu |
| E-mail(s) |
wjliu@xmu.edu.cn
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| Organization name |
xiamen university
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| Street address |
xiangan strict xiamen university
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| City |
xiamen |
| ZIP/Postal code |
361102 |
| Country |
China |
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| Platform ID |
GPL24688 |
| Series (2) |
| GSE167905 |
Identification of competing endogenous RNA (ceRNA) and micro-RNA profiles and regulatory networks in 4-nonylphenol-induced impairment of sertoli cells I |
| GSE167912 |
Identification of competing endogenous RNA (ceRNA) and micro-RNA profiles and regulatory networks in 4-nonylphenol-induced impairment of sertoli cells |
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| Relations |
| BioSample |
SAMN18090400 |
| SRA |
SRX10191143 |
| 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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