|
| Status |
Public on Jul 25, 2016 |
| Title |
HeLa-S3_parental_WT_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
HeLa-S3 cell, wild type
|
| 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, wild type
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
The low quality regions of raw reads were trimed with Btrim (http://graphics.med.yale.edu/trim/readme)
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 |
| E-mail(s) |
dokuzaki@biken.osaka-u.ac.jp
|
| 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 |
|
| Relations |
| BioSample |
SAMN03218133 |
| SRA |
SRX767064 |
