|
| Status |
Public on May 24, 2023 |
| Title |
pc9-sh-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC-9
shRNA: shSYK
gene abnormality: EGFR exon 19 deletion
|
| 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 |
S9S1
SYK knockdown of PC-9.
processed data file: PC9_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 |
SAMN10852644 |
| SRA |
SRX5315912 |
