GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1621377 Query DataSets for GSM1621377
Status Public on Jul 25, 2016
Title HeLa-S3_LATS2_KO+EV
Sample type SRA
Source name HeLa-S3 cell, LATS2 KO, rescued by empty vector, clone#3
Organism Homo sapiens
Characteristics cell line: HeLa-S3
tissue: cervix
trans-gene: empty vector
Treatment protocol no treatment
Growth protocol Add-back rescued LATS2 KO HeLa-S3 cells were cultured in DMEM + 10% fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100μg/mL) at 37°C, 5% CO2.
Extracted molecule total 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).
120 ng of each DNA 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
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 Feb 27, 2015
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)
GSE63538 LATS2 regulates repressive epigenetic integrity via regulation of Polycomb repressive complex 2
GSE66388 RNA-seq analysis of add-back rescued TALEN-mediated LATS2 knockout HeLa-S3 cells
BioSample SAMN03379995
SRA SRX893752

Supplementary file Size Download File type/resource
GSM1621377_KO+EV_FPKM.txt.gz 726.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap