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Status |
Public on Nov 30, 2018 |
Title |
ANT rep1 |
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 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) RNA-Seq, 20M clean reads
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
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: FPKM
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Submission date |
Nov 29, 2018 |
Last update date |
Nov 30, 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) |
GSE123113 |
RNA-seq reveals RNAs 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 |
SAMN10498154 |
SRA |
SRX5078315 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3495953_ANT-1.gene.fpkm.xls.gz |
1.9 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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