|
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.
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|
|
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.
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|
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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 |