|
| Status |
Public on Feb 26, 2020 |
| Title |
control_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Control RNA transfected
|
| Treatment protocol |
Lipofectamine 2000 (Invitrogen) was used to transfect A549 lung cancer cell line with 20nM miR-30a-5p, miR-30a-3p, or negative control RNA mimic (Dharmacon), according to the manufacturer’s protocol using the 6-well plate format. Triplicate samples were harvested 72 hours after transfection.
|
| Growth protocol |
A549 lung cell line was cultured in RPMI-1640 media supplemented with 10% FBS and penicillin/streptomycin and with additional L-glutamine. Cells were confirmed to be negative for mycoplasma.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from A549 cell line using Trizol (Invitrogen) according to the manufacturer’s protocol, with one exception. To enhance the isolation of small RNA, the isopropanol precipitation step was performed overnight at −20°C.
Libraries were made and RNA-seq profiles were generated by Novogene (https://en.novogene.com/). Illumina Novaseq 6000 system was used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequence mapping and quantification were performed using the methods STAR (V2.5) and HTSeq (V0.6.1), respectively. Standard pipeline of Novogene (https://en.novogene.com/) was used.
For sequence mapping, Human reference genome version hg19 was used.
The read counts were imported into edgeR for differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl gene ids, read counts, and FPKM values for each sample.
|
| |
|
| Submission date |
Dec 28, 2019 |
| Last update date |
Aug 17, 2022 |
| Contact name |
Ramkrishna Mitra |
| E-mail(s) |
ramkrishna.mitra@jefferson.edu
|
| Organization name |
Thomas Jefferson University
|
| Street address |
233 S 10th street
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE142695 |
Analysis of gene expression in lung adenocarcinoma cells following over-expression of miR-30a-5p or miR-30a-3p |
|
| Relations |
| BioSample |
SAMN13696457 |
| SRA |
SRX7473798 |
