|
| Status |
Public on May 26, 2020 |
| Title |
MUT2 |
| Sample type |
SRA |
| |
|
| Source name |
colon cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HCT-116
cell line: colon cancer cell line
genotype: 5'UTR-ORFmut
|
| 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 |
SAMN13113966 |
| SRA |
SRX7057686 |
