Comment[GEAAccession]	E-GEAD-366
MAGE-TAB Version	1.1
Investigation Title	Gene expression data of YAP1-knockdowned U2OS cells under heat shock stress
Experiment Description	Yes-associated protein 1 (YAP1), a co-transcription activator, shuttles between the cytoplasm and the nucleus. We found that when U2OS cells are exposed to 42 degree_C, YAP1 enters the nucleus within 30 min and returns to the cytoplasm at 4 h. To obtain better understanding of the role of YAP1 in the context of heat shock response, we performed Cap Analysis of Gene Expression (CAGE)-seq using samples of YAP1-knockdowned U2OS cells that were exposed to 42 degree_C for 2 h.
Experimental Design	case control design
Experimental Factor Name	knockdown
Experimental Factor Type	knockdown
Person Last Name	Maruyama
Person First Name	Junichi
Person Affiliation	Tokyo Medical and Dental University
Person Roles	submitter
Public Release Date	2020-06-02
Protocol Name	P-GEAD-484	P-GEAD-485	P-GEAD-486	P-GEAD-487	P-GEAD-488
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	U2OS cells were plated at 2.0 x 10^6 cells/well in a 60mm dish. To determine the implication of YAP1, cells were transfected with YAP1 siRNA in advance and 48 h later, exposed to heat shock.	Total RNAs were collected by using TRI Reagent (Molecular Research Center, Inc.) from cells with or without 2 h-heat shock.	A multiplexed CAGE library was constructed from 2.5 mg total RNA sample based on nAnT-iCAGE protocol by DNAFORM (Yokohama, Japan).	Multiplex deep sequencing of cDNA libraries was conducted on an Illumina NextSeq500 sequencer by DNAFORM.	The sequenced CAGE tags were mapped to mouse reference genomes, mm9, using the Burrows-Wheeler Aligner. Unmapped reads are mapped to mm9 using HiSAT2. For tag clustering, CAGE-tag 5'-coordinates were input for CAGEr clustering. Differential expression and motif discovery were analyzed by using R program DESeq2.
SDRF File	E-GEAD-366.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB9865
Comment[Last Update Date]	2020-06-02