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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 14, 2019 |
| Title |
OV 3 |
| Sample type |
SRA |
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| Source name |
SKOV3
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| Organism |
Homo sapiens |
| Characteristics |
genotype: CD83 stable overexpression
cell line: SKOV3
passage: <10
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| Treatment protocol |
To generate human CD83 stable overexpression or knockdown SKOV3 cell line, LV5-full length CD83 lentivirus (CD83-OV) or triple LV3-CD83-shRNA lentivirus (CD83-KD) (LV3-CD83-258, 5’-GCTCCGAAGATGTGGACTTGC-3’; LV3-CD83-486, 5’-GGACATACAGGTGCACTCTGC-3’; LV3-CD83-679, 5’-GCTACAGAGTATCTTCCCAGA-3’) was synthesized and constructed by GenePharma (Shanghai, China), respectively. LV5 or LV3 lentivirus, containing GFP and puromycin resistant site, was served as negative control (NC). Polybrene (4 μg/ml) was used to increase the lentivirus infection efficiency. Stable infected cell lines (GFP+) could be obtained by two rounds of 1 μg/ml puromycin selection.
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| Growth protocol |
The human EOC cell line SKOV3 44 (ATCC®HTB-77TM) was purchased from American Type Culture Collection (ATCC, VA, USA). Cells were cultured in McCoy’s 5a medium (Invitrogen, Beijing, China) containing 10% fetal bovine serum (Invitrogen), 1% penicillin/stretomycin (Invitrogen) at 37 °C with 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the CD83-OV, CD83-KD, and CD83-NC SKOV3 cells using TRNzol (Tiangen, Beijing, China).
RNA libraries were prepared for sequencing using standard BGI protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
SOAPnuke: v1.5.2, -l 15 -q 0.2 -n 0.05
HISAT2: v2.0.4, --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Bowtie2: v2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM: v1.2.12, default
DEGseq: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Genome_build: hg38
Supplementary_files_format_and_content: Including RPKM values for each sample
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| Submission date |
Jan 13, 2019 |
| Last update date |
Jan 14, 2019 |
| Contact name |
Su-Ren Chen |
| E-mail(s) |
chensuren@ioz.ac.cn
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| Organization name |
Institute of Zoology, Chinese Academy of Sciences
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| Department |
State Key Laboratory of Stem Cell and Reproductive Biology
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| Street address |
1Beichen West Road, Chaoyang District
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE125011 |
The Role of CD83 in ovarian cancer cell line SKOV3 |
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| Relations |
| BioSample |
SAMN10736297 |
| SRA |
SRX5245312 |
| 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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