|
Status |
Public on Jul 17, 2020 |
Title |
Non-synchronized_RNA-seq_CrMTA1_1 |
Sample type |
SRA |
|
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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
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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
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|
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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 |