Comment[GEAAccession]	E-GEAD-313
MAGE-TAB Version	1.1
Investigation Title	CAGE analysis of human dermal fibroblast after knock-down of lncRNAs (Set1-CAGE)
Experiment Description	To elucidate functions of lncRNAs, we performed knock-down experiments of hundreds of lncRNAs with human dermal fibroblast cell lines. After the knock-down, we profiled gene and promoter level expression profiles with the nAnTi-CAGE method.
Experimental Design	stimulus or stress design
Experimental Factor Name	perturb_id
Experimental Factor Type	perturb_id
Person Last Name	Kasukawa	Bono
Person First Name	Takeya	Hidemasa
Person Affiliation	RIKEN	
Person Roles	submitter	submitter
Public Release Date	2019-07-22
Protocol Name	P-GEAD-194	P-GEAD-195	P-GEAD-196	P-GEAD-197	P-GEAD-198	P-GEAD-199
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol	high throughput sequence alignment protocol
Protocol Description	To elucidate functions of lncRNAs, we performed knock-down experiments of hundreds of lncRNAs with human dermal fibroblast cell lines.  After the knock-down, we profiled gene and promoter level expression profiles with the nAnTi-CAGE method.	RNA from each fraction was isolated using Trizol LS (Invitrogen) according to manufacturer's instructions.	Four microgram of purified RNA was used to generate libraries according to the nAnT-iCAGE protocol (Murata et al. 2014). Briefly, random primer with anchor was used for cDNA synthesis, followed by biotinylation and RNaseI digestion. After cap trapping of the 5' end complete cDNA and linker ligation, second-strand was synthesized for dsDNA.	Libraries were combined in 8-plex using different barcodes and were subjected to 50-base single-end sequencing using an Illumina HiSeq 2500 instrument.	Expression tables are raw counts and normalized in TPM (Tags per million) with gene- and promoter-level	Tags were mapped to human genome assembly hg38 using TopHat 2.0.12.
SDRF File	E-GEAD-313.sdrf.txt
Comment[AEExperimentType]	CAGE
Comment[BioProject]	PRJDB7993
Comment[Last Update Date]	2019-08-14