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Sample GSM3517734 Query DataSets for GSM3517734
Status Public on Jul 17, 2020
Title Synchronized RNA-seq_CrMTA1_time_1
Sample type SRA
 
Source name colon
Organism Homo sapiens
Characteristics time point: 1
cell line: HCT116
tissue: colon
morphology: epithelial
disease: colorectal carcinoma
genotype/variation: MTA1-knockout
Treatment protocol For cell synchronization at the G1/S phase, 2 mM thymidine was used.
Growth protocol HCT116 were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (HyClone) and 1% penicillin/streptomycin (HyClone) at 37℃ in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent.Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH38 whole genome using hisat2 v2.1.0 with default parameters.
Transcript FPKM were calculated using Stringtie v1.3.4 with default parameters.
Genome_build: GRCH38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample
 
Submission date Dec 17, 2018
Last update date Jul 17, 2020
Contact name Haili Qian
E-mail(s) qianhaili@pumc.edu.cn
Organization name National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
Street address 17 South Panjiayuan Lane, Chaoyang District
City BEIJING
ZIP/Postal code 100021
Country China
 
Platform ID GPL20795
Series (2)
GSE123958 RNA-binding chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing [Synchronized RNA-seq]
GSE123959 RNA-binding chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing
Relations
BioSample SAMN10603305
SRA SRX5141904

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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