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Sample GSM2125378 Query DataSets for GSM2125378
Status Public on Jun 16, 2016
Title pCDNA-ctl
Sample type SRA
Source name Lung carcinoma cells
Organism Homo sapiens
Characteristics cell line: H157
cell type: Lung carcinoma cells
genotype/variation: expressing pCDNA-ctl
Treatment protocol The H157 lung carcinoma cells stably expressing different construct were collected after reaching mid-log growth phase, then subject to RNA purification
Growth protocol The H157 lung carcinoma cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.
Extracted molecule polyA RNA
Extraction protocol Total RNAs were purified from cells using Trizol method and subsequently cleaned using RNAeasy Kit.
Total RNA not exceeding 3 μg was further used to purify polyadenylated RNA using Illumina TruSeq Total RNA Sample Prep kits. We used the Ribo-Zero Human to remove cytoplasmic rRNA. The mRNA purified was further analyzed using Bioanalyzer (Agilent Technologies) prior to generation of cDNA library with bar coded ends. RNA-seq libraries were robotically prepared with Illumina TruSeq Total RNA Sample Prep kits according to the manufacturer’s protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Sequenced reads were aligned to hg19 using Bowtie v2.2.5
The EBSeq tool was used to identify differentially expressed genes in pairwise comparisons of all conditions
Genome_build: hg19
supplementary_files_format_and_content: Gene expression level of all conditions was merged to genes-merge.counts.matrix using rsem-generate-data-matrix. Scores represent expected reads count at each condition derived from rsem-calculate-expression
Submission date Apr 18, 2016
Last update date May 15, 2019
Contact name Zefeng Wang
Organization name CAS-MPG Partner Institute for Computational Biology (PICB)
Street address 320 Yueyang Road
City Shanghai
ZIP/Postal code 200031
Country China
Platform ID GPL18573
Series (1)
GSE80372 A splicing switch of TEAD4 regulates Hippo-YAP signaling pathway to inhibit tumor proliferation
BioSample SAMN04867264
SRA SRX1711020

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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