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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 15, 2019 |
| Title |
shNC |
| Sample type |
SRA |
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| Source name |
PLC/PRF/5 cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Liver cancer cell line
passages: 20-23
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina 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 |
Primary sequencing data is subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio. If alignment result passes QC, we will proceed with downstream analysis including gene expression and deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes and so on).
We define "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. They need to be removed before downstreamanalysis to decrease data noise.
We use Bowtie2 to map clean reads to reference gene and use HISAT to reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: Text files include RPKM values for each Sample
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| Submission date |
Jan 01, 2019 |
| Last update date |
May 15, 2019 |
| Contact name |
Weicheng Liang |
| E-mail(s) |
liangweicheng11@126.com
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| Phone |
96-13215464589
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| Organization name |
The Chinese University of Hong Kong
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| Street address |
Area 39
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| City |
Hong Kong |
| ZIP/Postal code |
852 |
| Country |
Hong Kong |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE124527 |
Global RNA expression profiles between shNC and shcircβ-catenin in PLC/PRF/5 cells |
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| Relations |
| BioSample |
SAMN10666590 |
| SRA |
SRX5192130 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3535855_shNC.gene.FPKM.txt.gz |
382.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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