Comment[GEAAccession]	E-GEAD-861
MAGE-TAB Version	1.1
Investigation Title	Gene expression analysis of ladinin-1 (LAD1) knockdown cancer cell
Experiment Description	RNA-seq for gene expression analysis of LAD1 knockdown HSC-4 by siRNA.
Experimental Design	cellular modification design
Experimental Factor Name	genetic_modification
Experimental Factor Type	genetic_modification
Person Last Name	Abe
Person First Name	Tatsuya
Person Affiliation	Graduate School of Medical and Dental Sciences Division of Oral Pathology, Niigata University
Person Roles	submitter
Public Release Date	2024-10-09
PubMed ID	39354061
Protocol Name	P-GEAD-3291	P-GEAD-3292	P-GEAD-3293	P-GEAD-3294	P-GEAD-3295
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	HSC-4, a human SCC cell line, was obtained from the RIKEN BRC Cell Bank. Stealth Select RNAi siRNAs against LAD1 (Invitrogen, Thermo Fisher Scientific), HSS105926, was used for LAD1. Negative Control High GC Duplex (Invitrogen) was used for the control.	Total RNA samples were isolated with RNeasy Plus Mini kit (Qiagen NV, Hilden, Germany).	NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra ll Directional RNA Library Prep Kit (New England Biolabs Inc., MA, USA) were used for poly-A selection and library preparation.	NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA) was used for sequencing.	After alinment by STAR (version 2.7.10b), read counts were generated by RSEM (version 1.3.3) with default parameters.
SDRF File	E-GEAD-861.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB16201
Comment[Last Update Date]	2024-10-09