|
| Status |
Public on Jul 29, 2014 |
| Title |
RBE-LKB1-2 |
| Sample type |
SRA |
| |
|
| Source name |
Intrahepatic cholangiocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Intrahepatic cholangiocarcinoma
sirna knockdown: LKB1 siRNA
cell line: RBE
time: 48h
|
| Treatment protocol |
45 pmal/6-well (5x10^5 cell) with 4.5 ul Lipofectamin RNAiMax following Lipofectamine® RNAiMAX Transfection Protocol
|
| Growth protocol |
HuH-28 cells were kept in MEM medium with 10% fetal bovine serum (FBS) +1% penicillin-streptomycin (P/S), all others were kept in RPMI1640 with the same supplements.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol RNA extraction protocol
Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2 (Illumia, San Diego, USA) with minor modifications.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling. Raw short sequence fragments were accepted if they passed the quality filtering parameters used in the Illumina GA Pipeline GERALD stage.
Sequenced reads were mapped to hg19 whole genome using tophat-1.2.0 with parameters -p 16 -g 10 -a 8
Aligned reads was normalized by edgeR bioconductor package and outputed as normalized RPKB file
Genome_build: Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: normalized RPKB in txt format for all 12 samples
|
| |
|
| Submission date |
Jul 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
keqiang zhang |
| Organization name |
City of Hope National Medical Center
|
| Department |
Molecular Pharmacology
|
| Street address |
1500 East Duarte Road
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE59855 |
Gene expression profiling associated with knockdown of LKB1 in human intrahepatic cholangiocarcinoma |
|
| Relations |
| BioSample |
SAMN02943497 |
| SRA |
SRX664963 |
