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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 30, 2018 |
| Title |
ANT rep1 [miRNA] |
| Sample type |
SRA |
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| Source name |
NCCIT tumor cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell type: TGCT cell line
tissue: Testis-derived
transfection: miR-125b antagomir
passage: <15
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| Treatment protocol |
NCCIT cells were transfected with the miR-125b antagomir (50 nM) or miR-125b agomir (25 nM) or non-targeting control (NC) oligonucleotides (25 nM) using EntransterTM-R4000 transfection reagent (Engreen, Beijing, China).
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| Growth protocol |
The human pluripotent embryonic carcinoma cell line NCCIT was purchased from ATCC (CRL-2073). NCCIT cells were cultured in RPMI 1640 (Invitrogen, Beijing, China) containing 10% fetal bovine serum (Invitrogen), 1% penicillin/stretomycin (Invitrogen) at 37oC with 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (including microRNAs) was extracted using miRcute miRNA Isolation Kit (Tiangen, Beijing, China).
Performed by BGI (Shenzhen, China)
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
BGISEQ-500 |
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| Data processing |
BGISEQ-500 platform
SOAPnuke, Version: v1.5.2, Parameter: -l 15 -q 0.2 -n 0.05, Webstite: https://github.com/BGI-flexlab/SOAPnuke
Bowtie2, Version: v2.2.5, Parameter: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, Website: http://bowtie-bio.sourceforge.net/Bowtie2/index.shtml
HISAT2, Version: v2.0.4, Parameter: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000, Website: http://0-www-ccb-jhu-edu.brum.beds.ac.uk/software/hisat
Genome_build: hg18
Supplementary_files_format_and_content: Gene expression files in excel format, read count, ratio
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| Submission date |
Nov 30, 2018 |
| Last update date |
Dec 03, 2018 |
| 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 (2) |
| GSE123156 |
microRNA-seq reveals microRNAs under the regulation of miR-125b in NCCIT tumor cells |
| GSE123157 |
RNA-seq and microRNA-seq reveal RNAs and microRNAs under the regulation of miR-125b in NCCIT tumor cells |
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| Relations |
| BioSample |
SAMN10502537 |
| SRA |
SRX5082761 |
| 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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