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Sample GSM3517720 Query DataSets for GSM3517720
Status Public on Jul 17, 2020
Title Non-synchronized_RNA-seq_CrMTA1_1
Sample type SRA
 
Source name colon
Organism Homo sapiens
Characteristics cell line: HCT116
tissue: colon
morphology: epithelial
disease: colorectal carcinoma
genotype/variation: MTA1 knockout
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 Illumina NextSeq 500
 
Data processing Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
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 GPL18573
Series (2)
GSE123957 RNA-binding chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing [Non-synchronized RNA-seq]
GSE123959 RNA-binding chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing
Relations
BioSample SAMN10603319
SRA SRX5141890

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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