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Sample GSM4140741 Query DataSets for GSM4140741
Status Public on May 26, 2020
Title NC1
Sample type SRA
 
Source name colon cancer cell line
Organism Homo sapiens
Characteristics cell type: HCT-116
cell line: colon cancer cell line
genotype: blank vector
Growth protocol These cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37℃ in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Illumina Casava1.7 software was used for basecalling.
Data filtering were performed as follows:1 ) Remove reads with adaptor sequences; 2). Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3). Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, this read is defined as low quality. No more than 2 mismatches were allowed in the alignment.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008)
Genome_build: GRCh38(hg38)
 
Submission date Oct 25, 2019
Last update date May 26, 2020
Contact name Guang-Rong Yan
E-mail(s) jxygr007@yahoo.com
Organization name Biomedicine Research Center, the Third Affiliated Hospital of Guangzhou Medical University
Street address 63 Duobao Road
City Guangzhou
State/province Guangdong
ZIP/Postal code 510150
Country China
 
Platform ID GPL24676
Series (1)
GSE139406 LOC90024-encoded small protein SRSP regulates mRNA splicing
Relations
BioSample SAMN13113973
SRA SRX7057679

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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