|
| Status |
Public on Feb 02, 2019 |
| Title |
miR-508 mimics, 2 |
| Sample type |
SRA |
| |
|
| Source name |
miR-508 mimics
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human colorectal cancer cells
cell line: HCT116
|
| Treatment protocol |
The adenovirus against human miR-508/508/509/514 mimics and miR-508 mimics were introduced into the HCT116 colorectal cells, while nonspecific microRNA virus was used as negative controls.
|
| Growth protocol |
The human colorectal cancer cells HCT116 were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA of HCT116 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA 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 HiSeq 3000 |
| |
|
| Description |
miR-508_genes.fpkm_tracking
M2
|
| Data processing |
Reads were mapped to the human genome (hg19) using TopHat v2.0.11 (http://tophat.cbcb.umd.edu) with the following default options with a TopHat transcript index built from Ensembl_GRCh37. Transcript expression was estimated with an improved version of Cuffdiff2 (http://cufflinks.cbcb.umd.edu). Cuffdiff was run with the default options against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html).
Genome_build: Ensembl_GRCh37(hg19)
Supplementary_files_format_and_content: HCT116_microRNA_mixure_genes.fpkm_tracking
Supplementary_files_format_and_content: miR-508_genes.fpkm_tracking
|
| |
|
| Submission date |
Feb 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Haoyan Chen |
| Organization name |
Renji Hospital
|
| Street address |
145 Shandong Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200001 |
| Country |
China |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE77462 |
Searching for target genes of miR-508/509/506/514 in HCT116 cells |
|
| Relations |
| BioSample |
SAMN04452399 |
| SRA |
SRX1557048 |
