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Sample GSM1551899 Query DataSets for GSM1551899
Status Public on Jul 25, 2016
Title HeLa-S3_LATS2_KO_RNA-seq
Sample type SRA
Source name HeLa-S3 cell, LATS2 KO
Organism Homo sapiens
Characteristics cell line: HeLa-S3
tissue: cervix
genotype: LATS2-/-
Treatment protocol no treatment
Growth protocol LATS2 KO HeLa-S3 cells and parental wild type cells were cultured in DMEM + 10% fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100μg/mL) at 37°C, 5% CO2.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from cultured cells with RNeasy Mini Kit (Qiagen) and processed according to the manufacturer’s protocol. The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA). After then, polyA RNA was isolated from the total RNA with Nucleo-Trap mRNA kit (Macherey-Nagel) and prepare the double-stranded cDNA using SuperScript Double-Stranded cDNA Synthesis kit (Life Technologies) according to manufacturer's instructions.
120 ng of each double-stranded cDNA was sheared to about 400 bp fragments using the Covaris S220 (Covaris) with following condition; peak incident power 140 W; duty factor 10%; cycles per burst 200; and treatment time 55 seconds. The resulting DNA fragments were purified using 0.7× volume Agencourt AMPureXP beads (Beckman Coulter). Illumina libraries were prepared using KAPA Library Preparation Kit (Kapa Biosystems) and TruSeq adaptors (Illumina) according to manufacturer’s instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description HeLa-S3 cell, LATS2 KO
Data processing Illumina Casava1.8.2 software used for basecalling.
The low quality regions of raw reads were trimed with Btrim (
The trimmed reads were mapped onto the reference human genome hg19 using TopHat ver.2.0.11 in combination with Bowtie ver. 2.2.2 and SAMtools ver. 0.1.19
Gene expression was quantified with Cufflinks ver. 2.2.1
Genome_build: hg19
Submission date Nov 21, 2014
Last update date May 15, 2019
Contact name Daisuke Okuzaki
Phone +81-6-6879-4935
Organization name Osaka univ.
Department Immunology Frontier Research Center
Lab Human Immunology (Single Cell Genomics)
Street address Yamadaoka 3-1
City Suita
State/province Osaka
ZIP/Postal code 565-0871
Country Japan
Platform ID GPL16791
Series (2)
GSE63537 RNA-seq analysis of TALEN-mediated LATS2 knockout HeLa-S3 cells
GSE63538 LATS2 regulates repressive epigenetic integrity via regulation of Polycomb repressive complex 2
BioSample SAMN03218131
SRA SRX767065

Supplementary file Size Download File type/resource
GSM1551899_KO_FPKM.txt.gz 731.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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