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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jan 14, 2019 |
Title |
KD 1 |
Sample type |
SRA |
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Source name |
SKOV3
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Organism |
Homo sapiens |
Characteristics |
genotype: CD83 stable knockdown 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 |
SAMN10736296 |
SRA |
SRX5245313 |
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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