NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3586038 Query DataSets for GSM3586038
Status Public on May 24, 2023
Title ebc1-sh-rep2
Sample type SRA
 
Source name cancer cells
Organism Homo sapiens
Characteristics cell line: EBC-1
shRNA: shSYK
gene abnormality: MET amplification
Growth protocol SYK in HCC827, PC-9 and EBC-1 cells was knocked down by an shRNA targeting SYK (shSYK, TRCN0000003166) engineered and packaged using a lentiviral delivery system. Corresponding negative controls were also generated. Cells were cultured as instructed.
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description E_662
SYK knockdown of EBC-1.
processed data file: EBC1_fpkm.txt
Data processing Illumina Casava software was used for basecalling.
Data filtering were performed as follows: 1) Remove reads with adaptor sequences; 2) Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3) Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 20) is greater than 50% in a read, this read is defined as low quality.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008).
Hisat2 (Kim D et al., 2015) was used to map clean reads to the reference genome of GRCh37 or GRch38 to map clean reads to reference gene.
Genome_build: GRCh38 (hg38) for HCC827, GRCh37 (hg19) for EBC-1 and PC-9
Supplementary_files_format_and_content: *_fpkm.txt: Tab-delimited text file includes FPKM values.
 
Submission date Jan 31, 2019
Last update date May 24, 2023
Contact name mengdi dai
E-mail(s) daimengdi@simm.ac.cn
Organization name SIMM
Street address 555 Zuchongzhi Rd, Bldg. 2, RM.409 shanghai, P.R. China
City Shanghai
State/province China
ZIP/Postal code 201203
Country China
 
Platform ID GPL20795
Series (1)
GSE125956 Transcriptomes change differently in different cancer cells upon SYK stable knockdown
Relations
BioSample SAMN10852637
SRA SRX5315919

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap