|
| Status |
Public on Jun 25, 2021 |
| Title |
RNA-Seq miR Control_1 |
| Sample type |
SRA |
| |
|
| Source name |
cultured fetal lung fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Fibroblast
cell culture: WI-38
treatment: control_miR
|
| Treatment protocol |
Cells were transfected with 50 nM control miRNA or anti-miR-340-5p and cultured for an additional four days, changing media every 48h (DMEM with 20% FBS).
|
| Growth protocol |
WI-38 fibroblasts were plated in a six-well plate at a density of 1 x 10^5 cells for 24h in DMEM + 20% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells using the TriPure isolation reagent (Roche) and the Direct-zol Mini Kit (Zymo) following the manufacturers’ protocols.
The total RNA purity and quantity were analyzed by RNA 6000 Nano LabChip Kit (Agilent, Palo Alto, CA, USA) and Bioanalyzer 2100 with RIN number >7.0. About 1 μg of RNA was used to construct small RNA library according to the protocol of Illumina’s TruSeq small RNA sample preparation Kits (San Diego, CA, USA). Sequencing was performed on Illumina HiSeq2500 with single-end mode (36bp SE).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
miR Control_1
|
| Data processing |
The RNA-seq reads were aligned to human genome hg19 using Spliced Transcripts Alignment to a Reference (STAR) software version 2.4.0j
featureCounts (v1.4.6-p5) were used to create gene counts
Differential expression analysis of gene counts was performed using the DESeq2 version 1.26.0
Genome_build: human genome hg19
Supplementary_files_format_and_content: text file
|
| |
|
| Submission date |
Jan 25, 2021 |
| Last update date |
Jun 25, 2021 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
|
| Department |
Laboratory of Genetics and Genomics
|
| Lab |
Computational Biology & Genomics Core
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE165466 |
Suppression of LBR by miR-340 disrupts chromatin, promotes cell senescence, and enhances senolysis (RNA-Seq 1) |
| GSE165469 |
Suppression of LBR by miR-340 disrupts chromatin, promotes cell senescence, and enhances senolysis |
|
| Relations |
| BioSample |
SAMN17530752 |
| SRA |
SRX9933113 |
