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Sample GSM1447488 Query DataSets for GSM1447488
Status Public on Jul 29, 2014
Title RBE-Control-1
Sample type SRA
Source name Intrahepatic cholangiocarcinoma
Organism Homo sapiens
Characteristics cell type: Intrahepatic cholangiocarcinoma
sirna knockdown: Control 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
BioSample SAMN02943494
SRA SRX664960

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

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