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| Status |
Public on Sep 22, 2017 |
| Title |
YAP_kd_RNA_rep3 |
| Sample type |
SRA |
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| Source name |
liver cancer cell
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Bel-7402
cell type: hepatocellular carcinoma
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| Growth protocol |
Bel-7402 cells were were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Hyclone, Logan, UT, USA) supplemented with 10% fetal bovine serum (FBS) (GIBCO, Carlsbad, CA, USA) and penicillin/streptomycin (GIBCO).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed in Bojian Biotechnology, Ltd using routine protocols.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
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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 |
Basecalls performed using CASAVA version 1.4
Raw RNA-seq reads were trimmed for adapter sequences, and marked for low-quality sequence. Then the clean reads were aligned to hg19 genome assembly and known junctions using Tophat v2.0.13 with default parameters.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were caculated using Cufflinks v2.2.1 with known genes annotation.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM abundance measurements
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| Submission date |
May 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Weisheng Zheng |
| E-mail(s) |
wisense@2008.sina.com
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| Organization name |
Tongji University
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| Department |
Department of Bioinformatics
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| Lab |
Jiang Lab
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| Street address |
Siping Road, No.1239
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (2) |
| GSE99313 |
Genome-wide analysis of YAP and TFCP2 down-regulated genes in liver cancer cells |
| GSE99315 |
Genome-wide analysis of YAP and TFCP2 occupancy and regulated expression in liver cancer cells |
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| Relations |
| BioSample |
SAMN07168877 |
| SRA |
SRX2858196 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2641028_YAPshl-3.genes.fpkm.txt.gz |
817.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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