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Sample GSM3535854 Query DataSets for GSM3535854
Status Public on Dec 31, 2019
Title siRNA-PiHL_rep3
Sample type SRA
Source name Colon cancer
Organism Homo sapiens
Characteristics cell line: HCT116
genotype/variation: siRNA-PiHL treatment
Treatment protocol HCT116 cells were treated with siRNA-NC or siRNA-PiHL
Growth protocol HCT116 cells were maintained at 37 °C in a humidified incubator containing 5% CO2 in Dulbecco’s modified Eagle medium (DMEM) (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (Gibco).
Extracted molecule total RNA
Extraction protocol Total RNA from each sample was extracted using Trizol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA purity was assessed by using an ND-1000 NanoDrop (Thermo Scientific, Wilmington, DE, USA). Each RNA sample had an A260:A280 ratio above 1.8 and an A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 Tape Station (Agilent Technologies, Santa Clara, CA, USA), and all samples had an RNA integrity value above 7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description siRNA-NC_rep3 vs. siRNA-PiHL_rep3
siRNA-PiHL treated HCT116 cells, replicate 3
Data processing HiSeq 3000 software was used for basecalling
Sequenced reads were mapped human transcriptome hg19 using TopHat 2.0.2 module
Transcripts were assembled and tested for abundance using Cufflinks 2.0.2 module
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM value for each sample
Submission date Jan 01, 2019
Last update date Dec 31, 2019
Contact name Xuan Deng
Organization name Huashan Hospital
Street address No.512 Huashan Road
City shanghai
ZIP/Postal code 200040
Country China
Platform ID GPL21290
Series (1)
GSE124526 A recurrently amplified long noncoding RNA in colorectal cancer regulates p53 protein stability through GRWD1/RPL11/MDM2 axis [RNA-seq]
BioSample SAMN10666583
SRA SRX5192121

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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